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Magnesium in PDB 1gpm: Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate

Enzymatic activity of Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate

All present enzymatic activity of Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate:
6.3.5.2;

Protein crystallography data

The structure of Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate, PDB code: 1gpm was solved by J.J.G.Tesmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 156.000, 102.000, 78.800, 90.00, 96.70, 90.00
R / Rfree (%) 17.4 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate (pdb code 1gpm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate, PDB code: 1gpm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1gpm

Go back to Magnesium Binding Sites List in 1gpm
Magnesium binding site 1 out of 3 in the Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg530

b:27.2
occ:0.54
O3 B:POP526 2.0 26.8 0.5
O1P B:AMP527 2.0 38.2 0.5
O6 B:POP526 2.0 38.9 0.5
O3P B:AMP527 2.1 38.0 0.5
O B:HOH609 2.1 26.4 0.7
P B:AMP527 2.5 38.8 0.5
P1 B:POP526 3.1 22.2 0.5
P2 B:POP526 3.3 39.1 0.5
O5' B:AMP527 3.3 34.8 0.5
O B:POP526 3.4 32.1 0.5
O1 B:POP526 3.7 23.3 0.5
O2P B:AMP527 3.9 39.3 0.5
O B:HOH557 3.9 62.6 0.6
C5' B:AMP527 4.0 30.8 0.5
O5 B:POP526 4.1 38.7 0.5
O2 B:POP526 4.2 18.8 0.5
OD2 B:ASP239 4.3 29.6 1.0
O4 B:POP526 4.5 35.5 0.5
O B:HOH635 4.5 34.1 0.5
O3' B:AMP527 4.8 27.1 0.5

Magnesium binding site 2 out of 3 in 1gpm

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Magnesium binding site 2 out of 3 in the Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg530

b:38.5
occ:0.72
O3 C:POP526 2.0 33.2 0.7
O C:HOH712 2.1 46.2 0.7
O6 C:POP526 2.1 45.4 0.7
O1P C:AMP527 2.1 42.8 0.5
P C:AMP527 3.1 44.0 0.5
P1 C:POP526 3.2 36.4 0.7
O5' C:AMP527 3.3 39.4 0.5
P2 C:POP526 3.3 41.3 0.7
O C:POP526 3.5 38.5 0.7
O3P C:AMP527 3.6 43.8 0.5
OD2 C:ASP239 3.8 18.5 1.0
O1 C:POP526 3.9 38.0 0.7
O4 C:POP526 4.1 44.3 0.7
O2 C:POP526 4.3 35.5 0.7
C5' C:AMP527 4.3 31.1 0.5
O2P C:AMP527 4.5 45.2 0.5
O5 C:POP526 4.5 44.9 0.7
CG C:ASP239 4.6 17.4 1.0
O3' C:AMP527 4.7 31.6 0.5
CB C:ASP239 4.8 17.4 1.0

Magnesium binding site 3 out of 3 in 1gpm

Go back to Magnesium Binding Sites List in 1gpm
Magnesium binding site 3 out of 3 in the Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli Gmp Synthetase Complexed with Amp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg530

b:40.3
occ:0.66
O3 D:POP526 2.0 39.9 0.7
O1P D:AMP527 2.0 39.8 0.4
O6 D:POP526 2.1 44.2 0.7
P2 D:POP526 3.3 43.8 0.7
P1 D:POP526 3.3 35.1 0.7
P D:AMP527 3.3 37.1 0.4
O5' D:AMP527 3.3 35.8 0.4
O D:POP526 3.4 35.3 0.7
OD2 D:ASP239 3.8 29.0 1.0
O1 D:POP526 4.0 35.7 0.7
O2P D:AMP527 4.1 37.0 0.4
O4 D:POP526 4.1 35.9 0.7
O D:HOH667 4.1 61.2 0.5
O2 D:POP526 4.3 25.3 0.7
O3P D:AMP527 4.3 34.6 0.4
O5 D:POP526 4.4 38.0 0.7
O3' D:AMP527 4.4 31.7 0.4
CG D:ASP239 4.7 28.1 1.0
C5' D:AMP527 4.7 33.3 0.4
CB D:ASP239 4.8 25.4 1.0

Reference:

J.J.Tesmer, T.J.Klem, M.L.Deras, V.J.Davisson, J.L.Smith. The Crystal Structure of Gmp Synthetase Reveals A Novel Catalytic Triad and Is A Structural Paradigm For Two Enzyme Families. Nat.Struct.Biol. V. 3 74 1996.
ISSN: ISSN 1072-8368
PubMed: 8548458
DOI: 10.1038/NSB0196-74
Page generated: Mon Dec 14 05:58:12 2020

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