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Magnesium in PDB 2ofw: Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules

Enzymatic activity of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules

All present enzymatic activity of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules:
2.7.1.25;

Protein crystallography data

The structure of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules, PDB code: 2ofw was solved by N.Sekulic, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.190, 69.030, 150.610, 90.00, 116.61, 90.00
R / Rfree (%) 21.7 / 28.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules (pdb code 2ofw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules, PDB code: 2ofw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2ofw

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:18.2
occ:1.00
 O B:HOH1290 1.8 24.9 1.0
O B:HOH1204 2.2 25.8 1.0
O B:HOH1203 2.3 21.4 1.0
OG1 B:THR66 2.3 22.1 1.0
O B:HOH1202 2.3 27.9 1.0
O2B B:ADX1201 2.3 22.0 1.0
SB B:ADX1201 3.4 23.2 1.0
O3B B:ADX1201 3.4 21.2 1.0
O B:HOH1205 3.6 25.4 1.0
O B:HOH1276 3.6 27.1 1.0
CB B:THR66 3.7 21.1 1.0
O B:HOH1261 3.8 32.3 1.0
OD2 B:ASP87 4.0 26.5 1.0
O2A B:ADX1201 4.1 24.4 1.0
N B:THR66 4.3 19.9 1.0
OE1 A:GLN31 4.3 46.9 1.0
O3' B:ADX1200 4.3 25.9 1.0
O1B B:ADX1201 4.3 24.0 1.0
OD1 B:ASP87 4.4 25.2 1.0
O B:HOH1243 4.5 36.6 1.0
CA B:THR66 4.5 21.7 1.0
NZ B:LYS171 4.5 30.0 1.0
CD A:GLN31 4.5 44.0 1.0
O3A B:ADX1201 4.6 22.2 1.0
CG2 B:THR66 4.6 21.6 1.0
CG B:ASP87 4.6 24.4 1.0
CE B:LYS65 4.6 18.0 1.0
O B:HOH1283 4.8 26.7 1.0
PA B:ADX1201 4.8 23.6 1.0
CG A:GLN31 4.9 43.9 1.0
NZ B:LYS65 4.9 16.8 1.0
NE2 A:GLN31 4.9 42.9 1.0
CB B:LYS65 4.9 19.3 1.0

Magnesium binding site 2 out of 6 in 2ofw

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:18.2
occ:1.00
 O C:HOH1304 2.1 20.3 1.0
O C:HOH1303 2.1 23.2 1.0
O C:HOH1302 2.2 28.8 1.0
OG1 C:THR66 2.2 20.5 1.0
O D:HOH1402 2.3 21.9 1.0
O2B C:ADX1301 2.4 19.8 1.0
CB C:THR66 3.5 20.7 1.0
SB C:ADX1301 3.5 18.6 1.0
O3B C:ADX1301 3.5 13.7 1.0
OD2 C:ASP89 3.7 25.1 1.0
O C:HOH1374 3.9 21.9 1.0
OD1 C:ASP87 4.0 22.9 1.0
O2A C:ADX1301 4.2 21.0 1.0
NE2 D:GLN31 4.2 35.6 1.0
OD2 C:ASP87 4.3 20.5 1.0
O C:HOH1333 4.3 31.9 1.0
N C:THR66 4.3 20.1 1.0
CG2 C:THR66 4.4 21.9 1.0
O3' C:ADX1300 4.5 26.4 1.0
CA C:THR66 4.5 20.9 1.0
O1B C:ADX1301 4.5 18.1 1.0
O3A C:ADX1301 4.6 18.2 1.0
CG C:ASP87 4.6 21.2 1.0
PA C:ADX1301 4.8 22.2 1.0
CG C:ASP89 4.8 21.1 1.0
CG D:GLN31 4.8 35.5 1.0
NZ C:LYS171 5.0 33.4 1.0
O C:SER130 5.0 17.5 1.0

Magnesium binding site 3 out of 6 in 2ofw

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:15.2
occ:1.00
 O D:HOH1406 1.7 23.1 1.0
OG1 D:THR66 2.0 21.0 1.0
O D:HOH1404 2.1 25.2 1.0
O D:HOH1403 2.1 16.8 1.0
O D:HOH1405 2.1 12.3 1.0
O2B D:ADX1401 2.2 25.0 1.0
CB D:THR66 3.2 21.9 1.0
SB D:ADX1401 3.4 22.2 1.0
O3B D:ADX1401 3.5 23.9 1.0
OD1 D:ASP87 3.9 20.5 1.0
OD1 D:ASP89 4.0 22.8 1.0
N D:THR66 4.0 21.0 1.0
OD2 D:ASP87 4.1 17.7 1.0
O D:HOH1442 4.1 27.7 1.0
O D:HOH1430 4.1 23.9 1.0
CG2 D:THR66 4.1 21.0 1.0
CA D:THR66 4.2 21.1 1.0
O2A D:ADX1401 4.2 25.1 1.0
O1B D:ADX1401 4.4 21.6 1.0
O3A D:ADX1401 4.4 25.5 1.0
CG D:ASP87 4.4 17.6 1.0
NE2 C:GLN31 4.5 29.0 1.0
PA D:ADX1401 4.7 27.6 1.0
CG C:GLN31 4.7 25.6 1.0
O3' D:ADX1400 4.7 22.4 1.0
O D:HOH1483 4.7 30.0 1.0
CD C:GLN31 4.9 27.7 1.0
CG D:ASP89 5.0 19.8 1.0
O1A D:ADX1401 5.0 26.7 1.0
CE D:LYS65 5.0 17.0 1.0

Magnesium binding site 4 out of 6 in 2ofw

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1005

b:27.6
occ:1.00
 O E:HOH1502 2.2 19.8 1.0
OG1 E:THR66 2.3 25.6 1.0
O2B E:ADX1501 2.3 20.2 1.0
O E:HOH1503 2.3 27.8 1.0
O E:HOH1504 2.6 31.4 1.0
O3B E:ADX1501 3.1 20.7 1.0
SB E:ADX1501 3.3 23.4 1.0
CB E:THR66 3.5 25.1 1.0
OD2 E:ASP89 3.7 24.0 1.0
O E:HOH1521 4.0 21.8 1.0
O E:HOH1534 4.0 23.4 1.0
O2A E:ADX1501 4.1 24.0 1.0
OD1 E:ASP87 4.1 25.8 1.0
N E:THR66 4.3 23.7 1.0
O1B E:ADX1501 4.3 25.0 1.0
OD2 E:ASP87 4.3 23.3 1.0
O3A E:ADX1501 4.4 23.8 1.0
O3' E:ADX1500 4.4 22.1 1.0
CG2 E:THR66 4.5 26.3 1.0
CA E:THR66 4.5 25.2 1.0
PA E:ADX1501 4.7 25.4 1.0
O E:HOH1582 4.7 25.5 1.0
CG E:ASP87 4.7 24.2 1.0
NE2 F:GLN31 4.7 35.6 1.0
CG E:ASP89 4.8 24.6 1.0
CG F:GLN31 4.9 37.4 1.0
NZ E:LYS65 4.9 23.9 1.0
CE E:LYS65 5.0 21.5 1.0

Magnesium binding site 5 out of 6 in 2ofw

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1006

b:19.3
occ:1.00
 O F:HOH1605 1.9 17.0 1.0
OG1 F:THR66 2.1 20.8 1.0
O F:HOH1602 2.1 22.5 1.0
O2B F:ADX1601 2.2 21.0 1.0
O F:HOH1603 2.4 20.0 1.0
O F:HOH1604 2.5 24.1 1.0
SB F:ADX1601 3.3 20.9 1.0
CB F:THR66 3.3 20.2 1.0
O3B F:ADX1601 3.4 19.2 1.0
OD2 F:ASP89 3.9 20.1 1.0
OD1 F:ASP87 3.9 21.0 1.0
O2A F:ADX1601 4.0 21.9 1.0
O F:HOH1669 4.1 26.9 1.0
O F:HOH1607 4.2 26.9 1.0
N F:THR66 4.2 20.3 1.0
OD2 F:ASP87 4.3 19.1 1.0
CG2 F:THR66 4.3 20.8 1.0
CA F:THR66 4.3 20.1 1.0
O3A F:ADX1601 4.3 21.7 1.0
O1B F:ADX1601 4.3 22.4 1.0
PA F:ADX1601 4.5 20.8 1.0
CG F:ASP87 4.5 19.1 1.0
O3' F:ADX1600 4.5 22.1 1.0
CG E:GLN31 4.7 29.5 1.0
NE2 E:GLN31 4.8 29.7 1.0
O1A F:ADX1601 4.8 22.2 1.0
O F:HOH1634 4.8 22.7 1.0
CG F:ASP89 4.9 20.5 1.0
CD E:GLN31 5.0 29.9 1.0
CE F:LYS65 5.0 23.9 1.0

Magnesium binding site 6 out of 6 in 2ofw

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Apsk Domain of Human PAPSS1 Complexed with 2 Aps Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1008

b:20.1
occ:1.00
 O2B H:ADX1801 2.1 25.8 1.0
O H:HOH1805 2.1 23.8 1.0
O H:HOH1803 2.2 24.7 1.0
O H:HOH1802 2.2 23.4 1.0
OG1 H:THR66 2.2 26.6 1.0
O H:HOH1903 2.4 41.7 1.0
SB H:ADX1801 3.3 24.4 1.0
CB H:THR66 3.4 25.6 1.0
O H:HOH1804 3.5 40.8 1.0
O3B H:ADX1801 3.5 21.3 1.0
OD1 H:ASP87 3.9 24.9 1.0
O2A H:ADX1801 3.9 27.5 1.0
OD1 H:ASP89 4.1 27.5 1.0
N H:THR66 4.1 24.5 1.0
O H:HOH1835 4.2 35.4 1.0
O1B H:ADX1801 4.3 22.8 1.0
CA H:THR66 4.3 25.7 1.0
OD2 H:ASP87 4.3 26.8 1.0
O3A H:ADX1801 4.4 25.1 1.0
CG2 H:THR66 4.4 25.7 1.0
NE2 G:GLN31 4.5 38.4 1.0
PA H:ADX1801 4.6 28.8 1.0
CG H:ASP87 4.6 24.1 1.0
O3' H:ADX1800 4.7 22.6 1.0
CG G:GLN31 4.9 37.9 1.0
CE H:LYS65 4.9 18.1 1.0
O H:HOH1840 5.0 38.5 1.0
CD G:GLN31 5.0 37.9 1.0

Reference:

N.Sekulic, K.Dietrich, I.Paarmann, S.Ort, M.Konrad, A.Lavie. Elucidation of the Active Conformation of the Aps-Kinase Domain of Human Paps Synthetase 1. J.Mol.Biol. V. 367 488 2007.
ISSN: ISSN 0022-2836
PubMed: 17276460
DOI: 10.1016/J.JMB.2007.01.025
Page generated: Wed Aug 14 01:26:59 2024

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