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Manganese in PDB 2ojw: Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate

Enzymatic activity of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate

All present enzymatic activity of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate:
6.3.1.2;

Protein crystallography data

The structure of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate, PDB code: 2ojw was solved by T.Karlberg, J.Uppenberg, C.Arrowsmith, H.Berglund, R.D.Busam, R.Collins, A.Edwards, S.Flodin, A.Flores, S.Graslund, B.M.Hallberg, M.Hammarstrom, M.Hogbom, I.Johansson, T.Kotenyova, M.Moche, M.E.Nilsson, P.Nordlund, T.Nyman, D.Ogg, C.Persson, J.Sagemark, P.Stenmark, M.Sundstrom, A.G.Thorsell, S.Van Den Berg, K.Wallden, J.Weigelt, L.Holmberg-Schiavone, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.25 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.600, 122.600, 126.600, 90.00, 130.60, 90.00
R / Rfree (%) 15.9 / 21.2

Other elements in 2ojw:

The structure of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate (pdb code 2ojw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 20 binding sites of Manganese where determined in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate, PDB code: 2ojw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 20 in 2ojw

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Manganese binding site 1 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:7.4
occ:1.00
 OE1 A:GLU203 2.1 6.9 1.0
OE2 A:GLU136 2.2 4.1 1.0
O2 A:PO4502 2.2 6.7 1.0
O A:HOH1686 2.3 4.2 1.0
OE1 A:GLU196 2.3 8.0 1.0
O4 A:PO4502 2.4 11.9 1.0
P A:PO4502 2.9 7.9 1.0
CD A:GLU203 3.1 7.8 1.0
CD A:GLU136 3.2 7.3 1.0
CD A:GLU196 3.2 8.6 1.0
MN A:MN404 3.5 13.3 0.8
CG A:GLU196 3.6 8.1 1.0
OE2 A:GLU203 3.6 10.4 1.0
O A:HOH1731 3.7 5.3 1.0
CG A:GLU136 3.8 4.8 1.0
MN A:MN403 3.8 6.9 1.0
O3 A:PO4502 4.0 6.1 1.0
O1 A:PO4502 4.0 3.5 1.0
OE1 A:GLU136 4.2 7.7 1.0
OE1 A:GLU134 4.2 6.6 1.0
OE2 A:GLU196 4.3 8.7 1.0
CG A:GLU203 4.3 8.4 1.0
CE1 A:HIS253 4.3 10.6 1.0
O A:HOH1504 4.4 5.7 1.0
O A:HOH1786 4.5 21.8 1.0
O A:HOH1635 4.6 7.4 1.0
ND2 A:ASN194 4.7 8.1 1.0
ND1 A:HIS253 4.7 9.0 1.0
CB A:GLU203 4.7 8.1 1.0
O A:HOH1730 4.9 18.9 1.0

Manganese binding site 2 out of 20 in 2ojw

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Manganese binding site 2 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:8.0
occ:1.00
 OE2 A:GLU338 2.0 12.2 1.0
O3B A:ADP501 2.1 4.7 1.0
OE1 A:GLU134 2.2 6.6 1.0
O1 A:PO4502 2.2 3.5 1.0
ND1 A:HIS253 2.5 9.0 1.0
OE2 A:GLU134 2.6 4.8 1.0
CD A:GLU134 2.7 6.2 1.0
CD A:GLU338 3.2 11.3 1.0
PB A:ADP501 3.3 6.4 1.0
CE1 A:HIS253 3.3 10.6 1.0
P A:PO4502 3.4 7.9 1.0
CG A:HIS253 3.5 10.9 1.0
O2 A:PO4502 3.6 6.7 1.0
O1B A:ADP501 3.6 10.0 1.0
NH1 A:ARG340 3.7 11.9 1.0
MN A:MN403 3.7 6.9 1.0
CB A:HIS253 3.8 9.5 1.0
OE1 A:GLU338 4.0 9.7 1.0
O A:HOH1686 4.0 4.2 1.0
NH1 A:ARG324 4.2 24.3 1.0
O3A A:ADP501 4.2 8.1 1.0
CG A:GLU134 4.2 7.5 1.0
CG A:GLU338 4.2 11.4 1.0
O A:HOH1540 4.2 10.1 1.0
O4 A:PO4502 4.3 11.9 1.0
O3 A:PO4502 4.4 6.1 1.0
NE2 A:HIS253 4.5 5.9 1.0
O2B A:ADP501 4.5 6.3 1.0
CD2 A:HIS253 4.6 8.1 1.0
O2A A:ADP501 4.7 6.8 1.0
CZ A:ARG340 4.7 13.6 1.0
CB A:GLU134 4.7 8.4 1.0

Manganese binding site 3 out of 20 in 2ojw

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Manganese binding site 3 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:6.9
occ:1.00
 O1B A:ADP501 2.0 10.0 1.0
O2A A:ADP501 2.2 6.8 1.0
O2 A:PO4502 2.2 6.7 1.0
OE2 A:GLU203 2.2 10.4 1.0
O A:HOH1635 2.3 7.4 1.0
OE1 A:GLU134 2.4 6.6 1.0
CD A:GLU203 3.2 7.8 1.0
PB A:ADP501 3.2 6.4 1.0
CD A:GLU134 3.3 6.2 1.0
PA A:ADP501 3.4 9.4 1.0
P A:PO4502 3.5 7.9 1.0
OE1 A:GLU203 3.5 6.9 1.0
O3A A:ADP501 3.6 8.1 1.0
O A:HOH1786 3.7 21.8 1.0
O3B A:ADP501 3.7 4.7 1.0
O A:HOH1686 3.7 4.2 1.0
MN A:MN402 3.7 8.0 1.0
O1 A:PO4502 3.8 3.5 1.0
MN A:MN401 3.8 7.4 1.0
CG A:GLU134 3.9 7.5 1.0
NE2 A:GLN205 4.1 5.1 1.0
OE2 A:GLU134 4.2 4.8 1.0
O3 A:PO4502 4.2 6.1 1.0
OD1 A:ASN194 4.2 5.8 1.0
O E:HOH1513 4.3 6.8 1.0
CB A:GLU134 4.4 8.4 1.0
O1A A:ADP501 4.4 8.7 1.0
O5' A:ADP501 4.4 5.7 1.0
O2B A:ADP501 4.5 6.3 1.0
CG A:GLU203 4.6 8.4 1.0
O4 A:PO4502 4.6 11.9 1.0
CD A:GLN205 4.8 9.9 1.0
CG A:GLN205 4.8 9.3 1.0

Manganese binding site 4 out of 20 in 2ojw

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Manganese binding site 4 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:13.3
occ:0.80
 O A:HOH1730 2.0 18.9 1.0
O A:HOH1729 2.2 16.5 1.0
O4 A:PO4502 2.2 11.9 1.0
OE1 A:GLU196 2.4 8.0 1.0
O A:HOH1731 2.5 5.3 1.0
CD A:GLU196 3.1 8.6 1.0
OE2 A:GLU196 3.1 8.7 1.0
P A:PO4502 3.4 7.9 1.0
MN A:MN401 3.5 7.4 1.0
O3 A:PO4502 3.6 6.1 1.0
OE2 A:GLU136 3.8 4.1 1.0
O E:HOH1702 4.2 19.9 1.0
O2 A:PO4502 4.2 6.7 1.0
CG A:GLU196 4.5 8.1 1.0
NH2 A:ARG340 4.5 12.4 1.0
O A:HOH1792 4.6 20.9 1.0
ND2 A:ASN248 4.6 16.8 1.0
OD2 E:ASP63 4.6 10.2 1.0
O1 A:PO4502 4.6 3.5 1.0
CG2 A:VAL197 4.8 8.1 1.0

Manganese binding site 5 out of 20 in 2ojw

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Manganese binding site 5 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:9.8
occ:1.00
 OE1 B:GLU203 2.0 11.1 1.0
OE2 B:GLU136 2.1 8.7 1.0
OE1 B:GLU196 2.2 10.2 1.0
O B:HOH1747 2.3 13.0 1.0
O3 B:PO4502 2.4 4.5 1.0
O4 B:PO4502 2.4 14.6 1.0
P B:PO4502 3.0 9.3 1.0
CD B:GLU203 3.1 9.7 1.0
CD B:GLU136 3.2 8.1 1.0
CD B:GLU196 3.3 10.9 1.0
MN B:MN404 3.4 16.5 0.8
OE2 B:GLU203 3.5 7.5 1.0
CG B:GLU196 3.7 8.2 1.0
O B:HOH1730 3.7 28.0 1.0
CG B:GLU136 3.8 7.3 1.0
MN B:MN403 3.8 8.5 1.0
O2 B:PO4502 4.0 10.8 1.0
O1 B:PO4502 4.0 11.1 1.0
OE1 B:GLU136 4.2 10.4 1.0
OE2 B:GLU134 4.2 10.2 1.0
CE1 B:HIS253 4.3 10.7 1.0
OE2 B:GLU196 4.3 10.5 1.0
CG B:GLU203 4.3 8.8 1.0
O B:HOH1512 4.5 12.1 1.0
O B:HOH1616 4.5 6.0 1.0
O B:HOH1740 4.6 18.2 1.0
ND1 B:HIS253 4.7 10.0 1.0
CB B:GLU203 4.8 7.1 1.0
ND2 B:ASN194 4.8 4.9 1.0

Manganese binding site 6 out of 20 in 2ojw

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Manganese binding site 6 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:10.9
occ:1.00
 OE2 B:GLU338 2.0 14.6 1.0
O2 B:PO4502 2.2 10.8 1.0
O2B B:ADP501 2.3 7.6 1.0
OE1 B:GLU134 2.4 6.2 1.0
OE2 B:GLU134 2.4 10.2 1.0
ND1 B:HIS253 2.5 10.0 1.0
CD B:GLU134 2.7 8.4 1.0
CD B:GLU338 3.3 12.6 1.0
CE1 B:HIS253 3.4 10.7 1.0
PB B:ADP501 3.4 10.8 1.0
P B:PO4502 3.4 9.3 1.0
CG B:HIS253 3.5 8.0 1.0
NH1 B:ARG340 3.6 10.7 1.0
O3 B:PO4502 3.7 4.5 1.0
O3B B:ADP501 3.8 9.0 1.0
MN B:MN403 3.8 8.5 1.0
CB B:HIS253 3.8 9.2 1.0
O B:HOH1747 3.9 13.0 1.0
OE1 B:GLU338 4.1 15.3 1.0
CG B:GLU338 4.2 13.0 1.0
CG B:GLU134 4.2 8.4 1.0
O3A B:ADP501 4.2 9.3 1.0
O4 B:PO4502 4.3 14.6 1.0
O B:HOH1589 4.4 11.8 1.0
O1 B:PO4502 4.5 11.1 1.0
NE2 B:HIS253 4.5 8.5 1.0
CD2 B:HIS253 4.6 7.8 1.0
O2A B:ADP501 4.6 5.5 1.0
O1B B:ADP501 4.7 12.9 1.0
CZ B:ARG340 4.7 12.3 1.0
CB B:GLU134 4.8 9.5 1.0

Manganese binding site 7 out of 20 in 2ojw

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Manganese binding site 7 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:8.5
occ:1.00
 O3 B:PO4502 2.1 4.5 1.0
O B:HOH1616 2.1 6.0 1.0
O3B B:ADP501 2.2 9.0 1.0
OE2 B:GLU134 2.2 10.2 1.0
O2A B:ADP501 2.2 5.5 1.0
OE2 B:GLU203 2.3 7.5 1.0
CD B:GLU203 3.2 9.7 1.0
PB B:ADP501 3.3 10.8 1.0
CD B:GLU134 3.3 8.4 1.0
PA B:ADP501 3.4 9.1 1.0
P B:PO4502 3.4 9.3 1.0
OE1 B:GLU203 3.5 11.1 1.0
O3A B:ADP501 3.6 9.3 1.0
O B:HOH1747 3.7 13.0 1.0
O2B B:ADP501 3.8 7.6 1.0
MN B:MN402 3.8 10.9 1.0
O2 B:PO4502 3.8 10.8 1.0
MN B:MN401 3.8 9.8 1.0
CG B:GLU134 4.0 8.4 1.0
NE2 B:GLN205 4.1 4.5 1.0
O1 B:PO4502 4.2 11.1 1.0
OE1 B:GLU134 4.2 6.2 1.0
O A:HOH1575 4.2 12.0 1.0
O1A B:ADP501 4.4 7.1 1.0
OD1 B:ASN194 4.4 7.1 1.0
O5' B:ADP501 4.4 8.9 1.0
O4 B:PO4502 4.5 14.6 1.0
CB B:GLU134 4.5 9.5 1.0
O1B B:ADP501 4.6 12.9 1.0
CG B:GLU203 4.6 8.8 1.0
CD B:GLN205 4.8 8.9 1.0
CG B:GLN205 4.8 9.3 1.0
O B:HOH1727 4.9 35.6 1.0

Manganese binding site 8 out of 20 in 2ojw

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Manganese binding site 8 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:16.5
occ:0.80
 O B:HOH1739 2.2 9.9 1.0
O B:HOH1730 2.2 28.0 1.0
O B:HOH1738 2.3 13.0 1.0
O B:HOH1740 2.3 18.2 1.0
O4 B:PO4502 2.3 14.6 1.0
OE1 B:GLU196 2.6 10.2 1.0
OE2 B:GLU196 3.1 10.5 1.0
CD B:GLU196 3.2 10.9 1.0
MN B:MN401 3.4 9.8 1.0
P B:PO4502 3.5 9.3 1.0
O1 B:PO4502 3.6 11.1 1.0
OE2 B:GLU136 3.8 8.7 1.0
O3 B:PO4502 4.2 4.5 1.0
O A:HOH1777 4.3 14.1 1.0
OD2 A:ASP63 4.5 9.8 1.0
O2 B:PO4502 4.6 10.8 1.0
ND2 B:ASN248 4.6 15.7 1.0
CG B:GLU196 4.7 8.2 1.0
NH2 B:ARG340 4.7 7.9 1.0
CG2 B:VAL197 4.8 6.5 1.0
CD B:GLU136 5.0 8.1 1.0

Manganese binding site 9 out of 20 in 2ojw

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Manganese binding site 9 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:11.1
occ:1.00
 OE2 C:GLU203 2.0 6.1 1.0
OE2 C:GLU136 2.1 10.8 1.0
O4 C:PO4502 2.2 9.2 1.0
O1 C:PO4502 2.3 5.0 1.0
O C:HOH1745 2.4 14.0 1.0
OE1 C:GLU196 2.4 14.0 1.0
P C:PO4502 2.9 7.9 1.0
CD C:GLU203 3.0 8.8 1.0
CD C:GLU136 3.2 9.5 1.0
CD C:GLU196 3.4 13.4 1.0
MN C:MN404 3.4 10.1 0.8
OE1 C:GLU203 3.5 8.3 1.0
O C:HOH1718 3.6 12.4 1.0
CG C:GLU136 3.7 7.2 1.0
CG C:GLU196 3.7 9.7 1.0
MN C:MN403 3.8 6.2 1.0
O2 C:PO4502 4.0 8.9 1.0
O3 C:PO4502 4.0 11.1 1.0
OE1 C:GLU136 4.1 8.2 1.0
CG C:GLU203 4.2 10.0 1.0
CE1 C:HIS253 4.2 9.5 1.0
OE1 C:GLU134 4.4 9.5 1.0
OE2 C:GLU196 4.4 13.6 1.0
O C:HOH1519 4.5 5.8 1.0
ND1 C:HIS253 4.6 10.1 1.0
ND2 C:ASN194 4.6 4.6 1.0
O B:HOH1741 4.7 9.2 1.0
CB C:GLU203 4.7 7.9 1.0
O C:HOH1604 4.7 6.2 1.0
O C:HOH1707 4.8 13.2 1.0

Manganese binding site 10 out of 20 in 2ojw

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Manganese binding site 10 out of 20 in the Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Human Glutamine Synthetase in Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:10.4
occ:1.00
 OE2 C:GLU338 2.0 11.5 1.0
O2B C:ADP501 2.1 7.4 1.0
OE1 C:GLU134 2.2 9.5 1.0
O3 C:PO4502 2.3 11.1 1.0
ND1 C:HIS253 2.5 10.1 1.0
OE2 C:GLU134 2.6 7.0 1.0
CD C:GLU134 2.7 9.3 1.0
CD C:GLU338 3.2 12.6 1.0
PB C:ADP501 3.4 6.5 1.0
P C:PO4502 3.4 7.9 1.0
CE1 C:HIS253 3.5 9.5 1.0
NH1 C:ARG340 3.5 12.0 1.0
CG C:HIS253 3.5 10.9 1.0
O1 C:PO4502 3.5 5.0 1.0
O3B C:ADP501 3.6 8.0 1.0
CB C:HIS253 3.8 10.2 1.0
MN C:MN403 3.8 6.2 1.0
OE1 C:GLU338 3.9 11.9 1.0
NH1 C:ARG324 4.0 23.0 1.0
O C:HOH1745 4.1 14.0 1.0
O3A C:ADP501 4.2 9.1 1.0
CG C:GLU338 4.2 12.4 1.0
CG C:GLU134 4.2 8.4 1.0
O C:HOH1603 4.2 8.8 1.0
O2 C:PO4502 4.4 8.9 1.0
O4 C:PO4502 4.4 9.2 1.0
O2A C:ADP501 4.5 8.4 1.0
O1B C:ADP501 4.6 6.8 1.0
CZ C:ARG340 4.6 10.2 1.0
NE2 C:HIS253 4.6 7.2 1.0
CD2 C:HIS253 4.6 11.2 1.0
CB C:GLU134 4.8 8.8 1.0
PA C:ADP501 5.0 10.5 1.0

Reference:

W.W.Krajewski, R.Collins, L.Holmberg-Schiavone, T.A.Jones, T.Karlberg, S.L.Mowbray. Crystal Structures of Mammalian Glutamine Synthetases Illustrate Substrate-Induced Conformational Changes and Provide Opportunities For Drug and Herbicide Design. J.Mol.Biol. V. 375 217 2008.
ISSN: ISSN 0022-2836
PubMed: 18005987
DOI: 10.1016/J.JMB.2007.10.029
Page generated: Sat Oct 5 14:45:54 2024

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