Magnesium in PDB 6rkc: Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum

Enzymatic activity of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum

All present enzymatic activity of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum:
2.5.1.6;

Protein crystallography data

The structure of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum, PDB code: 6rkc was solved by A.Shahar, R.Zarivach, S.Bershtein, D.Kleiner, F.Shmulevich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 2.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 142.372, 79.467, 143.787, 90.00, 105.11, 90.00
R / Rfree (%) 26 / 28.4

Other elements in 6rkc:

The structure of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum also contains other interesting chemical elements:

Potassium (K) 7 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum (pdb code 6rkc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum, PDB code: 6rkc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 6rkc

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Magnesium binding site 1 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:66.9
occ:1.00
 O2B A:PPK405 2.0 41.8 1.0
OD2 A:ASP18 2.4 37.0 1.0
O4A A:PPK405 2.4 41.6 1.0
O3G A:PPK405 2.6 43.5 1.0
K A:K401 2.7 50.5 1.0
CG A:ASP18 3.0 37.0 1.0
OD1 A:ASP18 3.0 37.3 1.0
O A:THR232 3.3 39.9 1.0
PB A:PPK405 3.5 42.5 1.0
OD2 A:ASP231 3.7 47.6 1.0
PA A:PPK405 3.8 42.6 1.0
O3A A:PPK405 3.9 42.8 1.0
PG A:PPK405 4.2 42.6 1.0
NH2 A:ARG237 4.3 36.6 1.0
OD1 A:ASP231 4.3 48.2 1.0
CG A:ASP231 4.4 47.8 1.0
CB A:ASP18 4.4 36.9 1.0
NZ A:LYS238 4.4 36.4 1.0
N3B A:PPK405 4.4 42.8 1.0
C A:THR232 4.5 39.8 1.0
CE1 A:HIS16 4.5 37.2 1.0
CZ A:ARG237 4.7 36.2 1.0
CA A:GLY233 4.8 37.9 1.0
O1B A:PPK405 4.8 43.3 1.0
O2A A:PPK405 4.8 42.2 1.0
NE A:ARG237 4.8 35.9 1.0
OE1 B:GLU44 4.8 48.4 1.0
O2G A:PPK405 4.9 42.2 1.0
O1A A:PPK405 4.9 42.9 1.0
CB A:ARG237 4.9 35.7 1.0

Magnesium binding site 2 out of 16 in 6rkc

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Magnesium binding site 2 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:37.7
occ:1.00
 O1A A:PPK409 2.4 36.1 1.0
O1G A:PPK409 2.5 38.6 1.0
OD2 A:ASP264 3.2 51.9 1.0
N3B A:PPK409 3.4 37.5 1.0
OD2 A:ASP113 3.6 43.1 1.0
PG A:PPK409 3.7 37.8 1.0
PA A:PPK409 3.7 36.3 1.0
OE1 B:GLU10 4.0 45.6 1.0
NZ B:LYS160 4.0 38.1 1.0
O A:GLN114 4.1 42.1 1.0
OE2 B:GLU10 4.1 45.6 1.0
CG A:ASP264 4.2 48.5 1.0
O3A A:PPK409 4.3 36.7 1.0
NZ B:LYS238 4.4 33.8 1.0
OD1 A:ASP264 4.5 49.1 1.0
CD B:GLU10 4.5 44.7 1.0
O4A A:PPK409 4.5 36.4 1.0
PB A:PPK409 4.6 36.8 1.0
CA A:GLY253 4.6 40.1 1.0
CG A:ASP113 4.7 43.4 1.0
O2G A:PPK409 4.7 38.5 1.0
O2A A:PPK409 4.7 36.1 1.0
CE B:LYS238 4.8 33.7 1.0
O3G A:PPK409 4.8 38.0 1.0
N A:GLY253 4.9 40.2 1.0
CE B:LYS160 5.0 37.7 1.0
CA A:GLY115 5.0 41.0 1.0

Magnesium binding site 3 out of 16 in 6rkc

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Magnesium binding site 3 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:39.9
occ:1.00
 O1G A:PPK405 2.1 42.4 1.0
O1A A:PPK405 2.5 42.9 1.0
OD2 B:ASP264 3.4 76.2 1.0
O A:HOH506 3.4 39.0 1.0
OD1 B:ASP264 3.6 73.6 1.0
PG A:PPK405 3.7 42.6 1.0
CG B:ASP264 3.9 67.2 1.0
N3B A:PPK405 3.9 42.8 1.0
OD2 B:ASP113 4.0 60.0 1.0
PA A:PPK405 4.0 42.6 1.0
O B:GLN114 4.0 51.4 1.0
OE1 A:GLU10 4.0 47.5 1.0
OE2 A:GLU10 4.1 46.5 1.0
CA B:GLY253 4.3 42.7 1.0
O3A A:PPK405 4.4 42.8 1.0
CD A:GLU10 4.4 45.9 1.0
N B:GLY253 4.6 43.1 1.0
O2G A:PPK405 4.6 42.2 1.0
NZ A:LYS238 4.6 36.4 1.0
O2A A:PPK405 4.7 42.2 1.0
CA B:GLY115 4.8 49.2 1.0
NZ A:LYS160 4.8 45.5 1.0
O3G A:PPK405 4.8 43.5 1.0
PB A:PPK405 4.8 42.5 1.0
O4A A:PPK405 4.9 41.6 1.0
CG B:ASP113 5.0 57.7 1.0

Magnesium binding site 4 out of 16 in 6rkc

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Magnesium binding site 4 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:60.0
occ:1.00
 OD2 B:ASP18 1.9 36.5 1.0
O2A A:PPK409 2.1 36.1 1.0
O1B A:PPK409 2.3 36.7 1.0
O3G A:PPK409 2.4 38.0 1.0
CG B:ASP18 2.6 36.6 1.0
OD1 B:ASP18 2.8 37.5 1.0
PA A:PPK409 3.4 36.3 1.0
K A:K408 3.5 57.4 1.0
O B:THR232 3.6 35.9 1.0
PB A:PPK409 3.6 36.8 1.0
OD2 B:ASP231 3.7 36.7 1.0
O3A A:PPK409 3.7 36.7 1.0
NZ B:LYS238 3.9 33.8 1.0
CB B:ASP18 3.9 36.2 1.0
PG A:PPK409 4.0 37.8 1.0
CE1 B:HIS16 4.1 34.9 1.0
O4A A:PPK409 4.3 36.4 1.0
NH2 B:ARG237 4.4 36.2 1.0
N3B A:PPK409 4.4 37.5 1.0
CG B:ASP231 4.5 37.1 1.0
OD1 B:ASP231 4.6 37.6 1.0
O1A A:PPK409 4.6 36.1 1.0
C B:THR232 4.7 35.8 1.0
CB B:ARG237 4.7 35.0 1.0
N B:ASP18 4.8 35.7 1.0
NE2 B:HIS16 4.8 35.0 1.0
CA B:ASP18 4.8 35.9 1.0
CA B:GLY233 4.8 35.0 1.0
CZ B:ARG237 4.8 36.2 1.0
NE B:ARG237 4.8 35.8 1.0
O2G A:PPK409 4.9 38.5 1.0
O2B A:PPK409 4.9 37.1 1.0

Magnesium binding site 5 out of 16 in 6rkc

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Magnesium binding site 5 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:40.0
occ:1.00
 OD2 C:ASP18 2.0 53.1 1.0
O2G C:PPK405 2.2 41.5 1.0
O2A C:PPK405 2.4 42.6 1.0
O1B C:PPK405 2.5 42.4 1.0
CG C:ASP18 2.7 51.4 1.0
OD1 C:ASP18 2.8 52.3 1.0
K C:K401 3.2 67.2 1.0
PB C:PPK405 3.7 43.0 1.0
PG C:PPK405 3.8 42.0 1.0
NH2 C:ARG237 3.8 49.8 1.0
PA C:PPK405 3.8 43.3 1.0
O C:THR232 3.9 52.0 1.0
O3A C:PPK405 4.0 43.2 1.0
NZ C:LYS238 4.0 50.0 1.0
CB C:ASP18 4.1 50.2 1.0
OD2 C:ASP231 4.2 54.8 1.0
NE C:ARG237 4.4 49.1 1.0
N3B C:PPK405 4.4 42.8 1.0
CZ C:ARG237 4.4 49.1 1.0
CB C:ARG237 4.4 48.7 1.0
CE1 C:HIS16 4.5 46.7 1.0
O1G C:PPK405 4.7 42.0 1.0
O3G C:PPK405 4.7 42.1 1.0
O4A C:PPK405 4.7 43.4 1.0
O1A C:PPK405 4.8 43.4 1.0
OD1 C:ASP231 4.9 54.6 1.0
CG C:ARG237 4.9 48.5 1.0
C C:THR232 5.0 51.3 1.0
CG C:ASP231 5.0 54.4 1.0
O C:ARG237 5.0 50.0 1.0
CA C:GLY233 5.0 50.2 1.0

Magnesium binding site 6 out of 16 in 6rkc

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Magnesium binding site 6 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:60.7
occ:1.00
 O4A C:PPK408 2.2 43.1 1.0
O3G C:PPK408 2.7 43.3 1.0
OD2 C:ASP264 2.9 58.2 1.0
OD2 C:ASP113 2.9 56.0 1.0
N3B C:PPK408 3.3 43.1 1.0
O C:GLN114 3.5 55.2 1.0
PA C:PPK408 3.5 42.7 1.0
OD1 C:ASP264 3.6 57.8 1.0
CG C:ASP264 3.6 58.2 1.0
O3A C:PPK408 3.7 42.8 1.0
NZ D:LYS160 3.8 49.9 1.0
PG C:PPK408 3.9 43.1 1.0
CG C:ASP113 4.0 55.8 1.0
PB C:PPK408 4.2 42.8 1.0
O1A C:PPK408 4.3 42.8 1.0
OE2 D:GLU10 4.4 65.8 1.0
O2A C:PPK408 4.5 42.3 1.0
CB C:ASP113 4.6 56.1 1.0
C C:GLN114 4.7 58.1 1.0
OE1 D:GLU10 4.7 63.2 1.0
OD1 C:ASP113 4.8 55.1 1.0
CA C:GLY115 4.9 59.7 1.0
O2G C:PPK408 4.9 42.5 1.0
CA C:GLY253 4.9 47.1 1.0
O1G C:PPK408 5.0 43.1 1.0
CE D:LYS160 5.0 50.1 1.0

Magnesium binding site 7 out of 16 in 6rkc

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Magnesium binding site 7 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg407

b:53.0
occ:1.00
 O1G C:PPK405 2.4 42.0 1.0
O C:HOH504 2.5 57.4 1.0
O4A C:PPK405 3.0 43.4 1.0
OD2 D:ASP264 3.1 52.7 1.0
OD1 D:ASP264 3.2 53.6 1.0
N3B C:PPK405 3.4 42.8 1.0
CG D:ASP264 3.5 53.6 1.0
PG C:PPK405 3.6 42.0 1.0
CA D:GLY253 3.6 46.8 1.0
N D:GLY253 3.8 47.3 1.0
OE1 C:GLU10 4.1 66.7 1.0
O3G C:PPK405 4.2 42.1 1.0
OE2 C:GLU10 4.3 65.3 1.0
C D:GLY252 4.4 47.3 1.0
PA C:PPK405 4.5 43.3 1.0
OD2 D:ASP113 4.6 56.6 1.0
O D:GLN114 4.7 54.9 1.0
CD C:GLU10 4.7 64.0 1.0
O D:GLY252 4.8 47.8 1.0
NZ C:LYS238 4.8 50.0 1.0
CB D:ASP264 4.9 53.4 1.0
O2G C:PPK405 4.9 41.5 1.0
PB C:PPK405 5.0 43.0 1.0

Magnesium binding site 8 out of 16 in 6rkc

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Magnesium binding site 8 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:39.7
occ:1.00
 O2G C:PPK408 2.0 42.5 1.0
OD2 D:ASP18 2.0 47.1 1.0
O2B C:PPK408 2.3 42.6 1.0
O2A C:PPK408 2.7 42.3 1.0
CG D:ASP18 2.8 47.2 1.0
OD1 D:ASP18 3.0 46.9 1.0
PG C:PPK408 3.5 43.1 1.0
NH2 D:ARG237 3.6 48.7 1.0
O D:HOH503 3.6 37.8 1.0
PB C:PPK408 3.6 42.8 1.0
NZ D:LYS238 3.9 44.6 1.0
NE D:ARG237 3.9 47.9 1.0
PA C:PPK408 4.0 42.7 1.0
N3B C:PPK408 4.0 43.1 1.0
CB D:ARG237 4.0 46.3 1.0
CZ D:ARG237 4.1 48.1 1.0
O3A C:PPK408 4.2 42.8 1.0
CB D:ASP18 4.3 47.8 1.0
O1G C:PPK408 4.3 43.1 1.0
O D:THR232 4.3 47.9 1.0
O D:ARG237 4.6 45.5 1.0
OD2 D:ASP231 4.6 55.4 1.0
O1B C:PPK408 4.6 43.0 1.0
CG D:ARG237 4.6 46.6 1.0
OE1 C:GLU44 4.6 52.7 1.0
O3G C:PPK408 4.7 43.3 1.0
O4A C:PPK408 4.8 43.1 1.0
CE1 D:HIS16 4.8 47.8 1.0
CD D:ARG237 5.0 47.1 1.0

Magnesium binding site 9 out of 16 in 6rkc

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Magnesium binding site 9 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:73.1
occ:1.00
 O4A E:PPK405 1.9 59.7 1.0
OD2 E:ASP18 2.1 66.4 1.0
O3G E:PPK405 2.4 62.2 1.0
O2B E:PPK405 2.5 60.9 1.0
CG E:ASP18 3.0 65.9 1.0
PA E:PPK405 3.1 59.9 1.0
O3A E:PPK405 3.2 60.6 1.0
OD1 E:ASP18 3.3 64.9 1.0
PB E:PPK405 3.3 61.3 1.0
OD2 E:ASP231 3.4 72.9 1.0
K E:K401 3.5 73.1 1.0
NZ E:LYS238 3.7 65.6 1.0
CE1 E:HIS16 3.8 75.5 1.0
O E:THR232 3.9 59.8 1.0
PG E:PPK405 3.9 61.9 1.0
O2A E:PPK405 4.1 60.8 1.0
CB E:ASP18 4.2 66.2 1.0
O1A E:PPK405 4.2 60.1 1.0
N3B E:PPK405 4.3 61.4 1.0
CG E:ASP231 4.3 71.7 1.0
OD1 E:ASP231 4.4 73.8 1.0
NE2 E:HIS16 4.4 75.7 1.0
O1B E:PPK405 4.7 60.9 1.0
NH2 E:ARG237 4.8 67.7 1.0
O2G E:PPK405 4.8 61.6 1.0
O1G E:PPK405 4.8 62.0 1.0
CE E:LYS238 4.9 65.0 1.0
ND1 E:HIS16 4.9 74.0 1.0
N E:ASP18 5.0 67.3 1.0

Magnesium binding site 10 out of 16 in 6rkc

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Magnesium binding site 10 out of 16 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:68.1
occ:1.00
 O1G E:PPK409 1.7 61.9 1.0
O1A E:PPK409 2.6 71.3 1.0
O F:HOH502 2.9 57.1 1.0
OD2 E:ASP264 2.9 77.8 1.0
PG E:PPK409 3.2 62.4 1.0
OD1 E:ASP264 3.3 70.0 1.0
CG E:ASP264 3.4 73.3 1.0
N3B E:PPK409 3.5 63.4 1.0
CA E:GLY253 3.5 65.0 1.0
O3G E:PPK409 3.7 63.0 1.0
N E:GLY253 3.8 63.7 1.0
PA E:PPK409 4.1 69.7 1.0
OE2 F:GLU10 4.3 66.2 1.0
C E:GLY252 4.4 64.6 1.0
O3A E:PPK409 4.5 66.9 1.0
OD2 E:ASP113 4.5 76.5 1.0
O2G E:PPK409 4.5 60.5 1.0
O E:GLN114 4.6 71.7 1.0
O2A E:PPK409 4.7 69.4 1.0
NZ F:LYS238 4.7 63.2 1.0
O E:GLY252 4.7 65.2 1.0
OE1 F:GLU10 4.7 67.9 1.0
CB E:ASP264 4.8 70.7 1.0
PB E:PPK409 4.9 64.1 1.0
CD F:GLU10 4.9 66.5 1.0
C E:GLY253 4.9 64.7 1.0

Reference:

D.Kleiner, F.Shmulevich, R.Zarivach, A.Shahar, M.Sharon, G.Ben-Nissan, S.Bershtein. The Inter-Dimeric Interface Controls Function and Stability of Ureaplasma Urealiticum Methionine S-Adenosyltransferase. J.Mol.Biol. 2019.
ISSN: ESSN 1089-8638
PubMed: 31520601
DOI: 10.1016/J.JMB.2019.09.003
Page generated: Mon Dec 14 23:59:54 2020

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