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Magnesium in PDB 2vd3: The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum

Enzymatic activity of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum

All present enzymatic activity of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum:
2.4.2.17;

Protein crystallography data

The structure of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum, PDB code: 2vd3 was solved by B.Lohkamp, T.Schweikert, A.J.Lapthorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.45
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 112.103, 112.103, 247.622, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 28.7

Other elements in 2vd3:

The structure of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum (pdb code 2vd3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum, PDB code: 2vd3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 2vd3

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Magnesium binding site 1 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1294

b:70.9
occ:1.00
 OD2 A:ASP158 2.2 53.5 1.0
CG A:ASP158 3.3 52.5 1.0
O A:LEU159 3.7 56.9 1.0
N A:LEU159 3.7 53.8 1.0
OD1 A:ASP158 3.8 53.7 1.0
OE2 A:GLU145 4.1 56.4 1.0
CB A:LEU159 4.3 55.5 1.0
CA A:LEU159 4.4 55.5 1.0
C A:LEU159 4.4 56.5 1.0
CB A:ASP158 4.6 52.1 1.0
CA A:ASP158 4.6 52.0 1.0
OE1 A:GLU119 4.6 48.4 1.0
C A:ASP158 4.7 52.9 1.0

Magnesium binding site 2 out of 9 in 2vd3

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Magnesium binding site 2 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1295

b:66.2
occ:0.50
 OE1 A:GLU82 2.8 49.1 1.0
O A:HOH2016 3.1 35.5 1.0
OE2 A:GLU82 3.2 48.0 1.0
CD A:GLU82 3.4 47.5 1.0
NH2 A:ARG188 4.1 46.7 1.0
OD2 A:ASP80 4.4 44.9 1.0
O A:VAL81 4.7 45.3 1.0
CG A:GLU82 4.8 47.3 1.0

Magnesium binding site 3 out of 9 in 2vd3

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Magnesium binding site 3 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1296

b:83.1
occ:1.00
 OE1 A:GLU22 2.5 53.6 1.0
NE2 A:GLN41 3.5 49.4 1.0
CD A:GLU22 3.5 52.2 1.0
CG A:GLN41 3.6 47.1 1.0
CA A:GLY27 3.6 47.2 1.0
O A:HOH2005 3.7 55.0 1.0
OE2 A:GLU22 3.7 54.5 1.0
CD A:GLN41 3.8 48.7 1.0
C A:GLY27 3.9 47.6 1.0
O A:LEU28 4.1 49.7 1.0
N A:GLY27 4.3 47.1 1.0
O A:GLY27 4.3 47.5 1.0
N A:LEU28 4.4 48.0 1.0
OE1 A:GLN41 4.8 49.4 1.0
CG A:GLU22 4.8 48.9 1.0
C A:LEU28 4.9 49.4 1.0

Magnesium binding site 4 out of 9 in 2vd3

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Magnesium binding site 4 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1297

b:71.1
occ:1.00
 OD1 A:ASP175 2.4 49.3 1.0
OD2 A:ASP175 2.9 50.3 1.0
CG A:ASP175 3.0 50.0 1.0
O A:THR176 3.8 46.8 1.0
CB A:ASP175 4.5 49.8 1.0
NE2 A:HIS131 4.6 59.4 1.0
N A:THR176 4.6 48.6 1.0
C A:THR176 4.9 47.4 1.0

Magnesium binding site 5 out of 9 in 2vd3

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Magnesium binding site 5 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1118

b:0.2
occ:1.00
 OE1 B:GLU136 3.6 57.4 1.0
OD1 A:ASP61 3.6 53.1 1.0
O A:HOH2007 4.0 49.0 1.0
CG2 B:VAL138 4.0 50.9 1.0
OE1 A:GLU57 4.2 52.8 1.0
CG A:ASP61 4.5 50.3 1.0
OD2 A:ASP61 4.5 52.8 1.0
CD B:GLU136 4.6 56.2 1.0
O A:HOH2015 4.8 35.3 1.0

Magnesium binding site 6 out of 9 in 2vd3

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Magnesium binding site 6 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1293

b:47.1
occ:1.00
 O B:LYS10 2.6 54.1 1.0
N B:ALA52 3.2 42.8 1.0
C B:LYS10 3.5 53.9 1.0
N B:LYS10 3.5 52.5 1.0
CA B:ARG51 3.6 44.1 1.0
CD B:ARG51 3.8 49.3 1.0
CB B:ALA52 3.8 42.3 1.0
N B:SER9 3.9 50.0 1.0
C B:ARG51 3.9 43.6 1.0
O B:SER50 3.9 44.9 1.0
CA B:LYS10 4.0 53.5 1.0
CG B:LYS10 4.0 54.0 1.0
CB B:PRO8 4.0 48.3 1.0
CA B:ALA52 4.1 42.4 1.0
CL B:CL1292 4.2 59.9 1.0
CA B:PRO8 4.2 48.3 1.0
OG B:SER9 4.4 50.3 1.0
CB B:ARG51 4.4 44.6 1.0
C B:PRO8 4.4 49.0 1.0
CG B:ARG51 4.6 46.1 1.0
N B:GLY11 4.6 54.6 1.0
C B:SER9 4.6 51.6 1.0
N B:ARG51 4.6 44.6 1.0
CB B:LYS10 4.6 53.6 1.0
C B:SER50 4.7 45.0 1.0
CA B:SER9 4.7 50.8 1.0
NE B:ARG51 4.8 51.5 1.0

Magnesium binding site 7 out of 9 in 2vd3

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Magnesium binding site 7 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1294

b:65.8
occ:1.00
 OD2 B:ASP158 2.4 52.2 1.0
OE2 B:GLU145 2.9 54.9 1.0
CG B:ASP158 3.3 53.3 1.0
OD1 B:ASP158 3.4 55.6 1.0
CD B:GLU145 3.9 54.4 1.0
CG B:GLU145 4.3 53.5 1.0
OG1 B:THR144 4.3 51.8 1.0
OE1 B:GLU119 4.6 47.8 1.0
CB B:ASP158 4.7 52.4 1.0
N B:LEU159 4.9 53.8 1.0
OE1 B:GLU145 4.9 54.8 1.0

Magnesium binding site 8 out of 9 in 2vd3

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Magnesium binding site 8 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1295

b:64.2
occ:1.00
 O B:GLY11 2.1 55.6 1.0
N B:GLU15 3.2 50.8 1.0
C B:GLY11 3.3 55.5 1.0
CB B:SER14 3.5 51.7 1.0
N B:SER14 3.5 52.5 1.0
CA B:ARG12 3.6 56.2 1.0
C B:ARG12 3.7 55.6 1.0
CA B:SER14 3.8 51.8 1.0
N B:ARG12 3.9 55.8 1.0
CB B:GLU15 3.9 50.1 1.0
C B:SER14 4.0 51.5 1.0
O B:ARG12 4.0 55.9 1.0
CG B:GLU15 4.1 51.0 1.0
CD B:PRO16 4.1 48.7 1.0
CA B:GLU15 4.2 50.3 1.0
N B:ILE13 4.2 54.7 1.0
C B:ILE13 4.5 53.3 1.0
CA B:GLY11 4.5 55.0 1.0
OG B:SER14 4.6 51.8 1.0
N B:GLY11 4.6 54.6 1.0
CD B:GLU15 4.7 51.6 1.0
OE1 B:GLU15 4.7 53.0 1.0
CB B:ARG12 4.9 56.4 1.0
CA B:ILE13 5.0 53.9 1.0

Magnesium binding site 9 out of 9 in 2vd3

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Magnesium binding site 9 out of 9 in the The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1296

b:69.2
occ:1.00
 O B:HOH2006 2.4 63.9 1.0
OG B:SER9 2.4 50.3 1.0
O B:HOH2001 2.6 78.7 1.0
CB B:SER9 3.4 51.0 1.0
CG B:ARG51 3.9 46.1 1.0
N B:ARG51 4.1 44.6 1.0
C B:SER50 4.3 45.0 1.0
CD B:ARG51 4.4 49.3 1.0
CA B:SER50 4.6 45.3 1.0
CA B:ARG51 4.7 44.1 1.0
CA B:SER9 4.7 50.8 1.0
NH2 B:ARG51 4.7 52.9 1.0
O B:SER50 4.8 44.9 1.0
O B:PHE49 4.8 45.8 1.0
CB B:ARG51 4.9 44.6 1.0
O B:HOH2007 4.9 41.7 1.0
N B:SER50 4.9 45.5 1.0

Reference:

B.Lohkamp, T.Schweikert, A.J.Lapthorn. The Structure of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum To Be Published.
Page generated: Wed Aug 14 05:07:45 2024

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