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Magnesium in PDB 4gp2: Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium

Protein crystallography data

The structure of Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium, PDB code: 4gp2 was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, C.D.Poulter, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.991, 93.559, 146.886, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium (pdb code 4gp2). 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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium, PDB code: 4gp2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4gp2

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Magnesium binding site 1 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:42.9
occ:1.00
 O A:HOH561 2.0 42.7 1.0
O1B A:DMA403 2.0 53.1 1.0
OD2 A:ASP85 2.0 38.9 1.0
O A:HOH591 2.1 41.8 1.0
O1A A:DMA403 2.1 41.8 1.0
OD2 A:ASP89 2.2 42.9 1.0
CG A:ASP85 3.0 37.7 1.0
MG A:MG402 3.2 45.4 1.0
CG A:ASP89 3.2 42.9 1.0
OD1 A:ASP85 3.4 39.8 1.0
PB A:DMA403 3.4 65.3 1.0
PA A:DMA403 3.4 48.4 1.0
CB A:ASP89 3.6 38.0 1.0
O3A A:DMA403 3.6 59.4 1.0
NH2 A:ARG94 4.1 49.0 1.0
O A:ASP85 4.1 36.3 1.0
C1 A:DMA403 4.2 65.0 1.0
O1 A:DMA403 4.3 70.7 1.0
O2B A:DMA403 4.3 83.4 1.0
CB A:ASP85 4.3 29.9 1.0
OD1 A:ASP86 4.3 43.0 1.0
OD1 A:ASP89 4.4 36.3 1.0
O A:HOH584 4.4 43.8 1.0
O3B A:DMA403 4.4 64.3 1.0
C A:ASP85 4.4 38.8 1.0
O2A A:DMA403 4.7 56.4 1.0
O A:HOH574 4.8 44.1 1.0
O A:HOH585 4.9 46.1 1.0
N A:ASP86 4.9 32.6 1.0
CA A:ASP85 5.0 32.1 1.0

Magnesium binding site 2 out of 6 in 4gp2

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Magnesium binding site 2 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:45.4
occ:1.00
 O A:HOH574 2.0 44.1 1.0
OD2 A:ASP89 2.1 42.9 1.0
O A:HOH584 2.1 43.8 1.0
O1A A:DMA403 2.1 41.8 1.0
OD1 A:ASP85 2.2 39.8 1.0
O A:HOH585 2.2 46.1 1.0
CG A:ASP89 3.0 42.9 1.0
CG A:ASP85 3.1 37.7 1.0
OD1 A:ASP89 3.2 36.3 1.0
MG A:MG401 3.2 42.9 1.0
PA A:DMA403 3.3 48.4 1.0
OD2 A:ASP85 3.4 38.9 1.0
OE1 A:GLU148 3.8 45.8 1.0
O2A A:DMA403 3.8 56.4 1.0
O A:HOH576 3.8 51.7 1.0
O1 A:DMA403 3.9 70.7 1.0
OE2 A:GLU148 4.0 43.4 1.0
O A:HOH591 4.0 41.8 1.0
C1 A:DMA403 4.1 65.0 1.0
CD A:GLU148 4.3 60.0 1.0
CB A:ASP89 4.4 38.0 1.0
CB A:ASP85 4.5 29.9 1.0
OD2 A:ASP151 4.5 52.4 1.0
O1B A:DMA403 4.6 53.1 1.0
O3A A:DMA403 4.7 59.4 1.0
C2 A:DMA403 4.8 82.2 1.0
NH2 A:ARG159 4.8 40.4 1.0
O A:ASP85 4.8 36.3 1.0
NZ A:LYS249 4.9 49.8 1.0
O A:HOH561 4.9 42.7 1.0

Magnesium binding site 3 out of 6 in 4gp2

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Magnesium binding site 3 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:45.7
occ:1.00
 OD2 A:ASP229 2.0 46.5 1.0
O A:HOH543 2.1 41.0 1.0
O A:HOH594 2.1 43.6 1.0
OD2 A:ASP225 2.2 39.4 1.0
O A:HOH575 2.2 39.1 1.0
O A:HOH582 2.2 43.0 1.0
CG A:ASP229 3.2 44.6 1.0
CG A:ASP225 3.3 53.5 1.0
CB A:ASP229 3.8 43.6 1.0
OD1 A:ASP225 3.9 48.7 1.0
O A:HOH614 4.0 52.8 1.0
OD1 A:ASP244 4.2 42.9 1.0
OD2 A:ASP244 4.2 40.9 1.0
NE2 A:GLN222 4.2 36.9 1.0
OD1 A:ASP229 4.2 51.8 1.0
O A:ASP225 4.2 36.7 1.0
O A:HOH632 4.3 56.5 1.0
OD1 A:ASP226 4.4 36.4 1.0
NZ A:LYS243 4.4 54.3 1.0
CB A:ASP225 4.5 39.6 1.0
C A:ASP225 4.5 38.2 1.0
O A:HOH615 4.6 57.4 1.0
CG A:ASP244 4.6 45.1 1.0
N A:ASP226 4.9 35.1 1.0

Magnesium binding site 4 out of 6 in 4gp2

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Magnesium binding site 4 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:40.2
occ:1.00
 O B:HOH566 2.0 38.2 1.0
O B:HOH565 2.1 40.1 1.0
O B:HOH567 2.1 37.8 1.0
O2A B:DMA404 2.1 37.6 1.0
OD2 B:ASP89 2.1 36.0 1.0
OD1 B:ASP85 2.2 37.4 1.0
CG B:ASP89 3.1 47.8 1.0
PA B:DMA404 3.1 49.1 1.0
CG B:ASP85 3.2 37.6 1.0
MG B:MG402 3.2 40.3 1.0
OD1 B:ASP89 3.3 36.1 1.0
OD2 B:ASP85 3.4 34.1 1.0
O1 B:DMA404 3.5 57.6 1.0
O1A B:DMA404 3.6 53.7 1.0
OE1 B:GLU148 3.9 43.7 1.0
OE2 B:GLU148 4.0 40.3 1.0
O B:HOH596 4.1 44.4 1.0
O B:HOH593 4.1 43.4 1.0
OD2 B:ASP151 4.2 45.5 1.0
C1 B:DMA404 4.2 63.8 1.0
CD B:GLU148 4.4 55.1 1.0
O B:HOH569 4.4 47.4 1.0
CB B:ASP89 4.5 40.6 1.0
CB B:ASP85 4.6 27.5 1.0
O3A B:DMA404 4.6 50.0 1.0
O3B B:DMA404 4.6 46.8 1.0
NZ B:LYS249 4.7 42.6 1.0
O B:ASP85 4.9 35.9 1.0
C2 B:DMA404 4.9 72.2 1.0

Magnesium binding site 5 out of 6 in 4gp2

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Magnesium binding site 5 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:40.3
occ:1.00
 O2A B:DMA404 2.0 37.6 1.0
O3B B:DMA404 2.0 46.8 1.0
OD2 B:ASP85 2.1 34.1 1.0
O B:HOH564 2.1 39.2 1.0
O B:HOH593 2.3 43.4 1.0
OD2 B:ASP89 2.3 36.0 1.0
CG B:ASP85 3.1 37.6 1.0
MG B:MG401 3.2 40.2 1.0
PA B:DMA404 3.3 49.1 1.0
PB B:DMA404 3.3 59.8 1.0
CG B:ASP89 3.3 47.8 1.0
OD1 B:ASP85 3.4 37.4 1.0
O3A B:DMA404 3.6 50.0 1.0
CB B:ASP89 3.6 40.6 1.0
NH2 B:ARG94 3.9 42.0 1.0
O2B B:DMA404 3.9 58.1 1.0
O B:HOH567 4.1 37.8 1.0
O B:ASP85 4.2 35.9 1.0
O B:HOH597 4.2 45.1 1.0
O1 B:DMA404 4.2 57.6 1.0
C1 B:DMA404 4.4 63.8 1.0
CB B:ASP85 4.4 27.5 1.0
OD1 B:ASP89 4.4 36.1 1.0
O1A B:DMA404 4.4 53.7 1.0
O1B B:DMA404 4.5 53.1 1.0
C B:ASP85 4.5 43.5 1.0
OD1 B:ASP86 4.5 41.1 1.0
O B:HOH569 4.7 47.4 1.0
O B:HOH566 4.9 38.2 1.0
O B:HOH565 4.9 40.1 1.0
N B:ASP86 5.0 34.4 1.0

Magnesium binding site 6 out of 6 in 4gp2

Go back to Magnesium Binding Sites List in 4gp2
Magnesium binding site 6 out of 6 in the Crystal Structure of Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium


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 Isoprenoid Synthase A3MSH1 (Target Efi-501992) From Pyrobaculum Calidifontis Complexed with Dmapp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:48.4
occ:1.00
 OD2 B:ASP229 1.9 50.5 1.0
O B:HOH576 2.1 49.7 1.0
O B:HOH574 2.1 44.2 1.0
O B:HOH575 2.1 42.8 1.0
O B:HOH544 2.2 44.7 1.0
OD2 B:ASP225 2.3 50.8 1.0
CG B:ASP229 3.0 64.9 1.0
CG B:ASP225 3.3 60.0 1.0
O B:HOH609 3.6 57.1 1.0
CB B:ASP229 3.8 37.2 1.0
OD1 B:ASP225 3.8 48.7 1.0
NZ B:LYS243 3.9 69.2 1.0
OD1 B:ASP229 4.0 47.5 1.0
OD1 B:ASP244 4.2 44.9 1.0
NE2 B:GLN222 4.2 35.0 1.0
O B:HOH602 4.2 63.5 1.0
OD2 B:ASP244 4.2 39.3 1.0
O B:ASP225 4.3 37.2 1.0
OD1 B:ASP226 4.4 37.1 1.0
CB B:ASP225 4.5 36.2 1.0
C B:ASP225 4.6 39.1 1.0
CG B:ASP244 4.7 43.3 1.0
O2B B:DMA404 4.8 58.1 1.0
CE B:LYS243 4.9 83.7 1.0
O B:HOH594 4.9 50.9 1.0
O1A B:DMA404 5.0 53.7 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, C.D.Poulter, J.A.Gerlt, S.C.Almo. Crystal Structure of Isoprenoid Synthase From Pyrobaculum Calidifontis To Be Published.
Page generated: Mon Aug 11 13:36:46 2025

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