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Magnesium in PDB 2yxh: Crystal Structure of Mazg-Related Protein From Thermotoga Maritima

Protein crystallography data

The structure of Crystal Structure of Mazg-Related Protein From Thermotoga Maritima, PDB code: 2yxh was solved by B.Padmanabhan, Y.Bessho, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.829, 56.788, 61.615, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima (pdb code 2yxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima, PDB code: 2yxh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2yxh

Go back to Magnesium Binding Sites List in 2yxh
Magnesium binding site 1 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


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 Mazg-Related Protein From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:33.2
occ:1.00
O A:HOH607 2.0 27.5 1.0
OE2 A:GLU34 2.0 30.6 1.0
O A:HOH608 2.1 38.0 1.0
O A:HOH569 2.1 37.1 1.0
O A:HOH609 2.2 31.8 1.0
OD2 A:ASP60 2.2 27.5 1.0
CD A:GLU34 3.1 29.9 1.0
CG A:ASP60 3.1 30.9 1.0
OD1 A:ASP60 3.2 32.4 1.0
CG A:GLU34 3.5 30.5 1.0
O A:HOH605 3.9 24.6 1.0
O A:HOH542 4.1 50.7 1.0
O A:HOH573 4.1 37.8 1.0
OE1 A:GLU34 4.2 31.0 1.0
O A:HOH602 4.3 47.7 1.0
O A:ALA30 4.5 32.6 1.0
CB A:ASP60 4.5 25.8 1.0
CB A:ALA30 4.7 31.6 1.0
O A:ASP56 4.9 24.1 1.0
CB A:GLU34 4.9 28.3 1.0
C A:ALA30 5.0 32.1 1.0

Magnesium binding site 2 out of 4 in 2yxh

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


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 Mazg-Related Protein From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.2
occ:1.00
OD2 A:ASP56 1.9 31.2 1.0
OE2 A:GLU37 2.0 41.6 1.0
OE1 A:GLU53 2.1 27.1 1.0
OE1 A:GLU34 2.2 31.0 1.0
O A:HOH605 2.3 24.6 1.0
O A:HOH606 2.3 27.7 1.0
CG A:ASP56 2.9 22.5 1.0
CD A:GLU53 3.1 26.1 1.0
CD A:GLU34 3.2 29.9 1.0
CD A:GLU37 3.3 44.4 1.0
CB A:ASP56 3.3 23.4 1.0
OE2 A:GLU53 3.4 27.1 1.0
OE2 A:GLU34 3.4 30.6 1.0
O A:HOH570 3.9 57.3 1.0
OE1 A:GLU37 3.9 48.5 1.0
O B:HOH614 3.9 39.0 1.0
OD1 A:ASP56 4.0 31.2 1.0
OE2 A:GLU52 4.1 44.9 1.0
NZ B:LYS86 4.2 29.4 1.0
O A:HOH573 4.3 37.8 1.0
CB A:GLU37 4.4 32.9 1.0
CG A:GLU37 4.4 34.4 1.0
O A:HOH555 4.4 49.2 1.0
CG A:GLU53 4.4 21.3 1.0
CA A:GLU53 4.5 24.4 1.0
CG A:GLU34 4.6 30.5 1.0
CB A:GLU53 4.7 26.3 1.0
CD A:GLU52 4.8 35.0 1.0
CA A:ASP56 4.8 22.6 1.0
CB A:GLU34 4.9 28.3 1.0

Magnesium binding site 3 out of 4 in 2yxh

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


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 Mazg-Related Protein From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:31.6
occ:1.00
O B:HOH626 1.9 40.6 1.0
OE2 B:GLU34 2.0 31.1 1.0
O B:HOH523 2.1 28.9 1.0
O B:HOH620 2.1 35.3 1.0
O B:HOH507 2.1 23.3 1.0
OD2 B:ASP60 2.3 30.3 1.0
CD B:GLU34 3.0 35.2 1.0
CG B:ASP60 3.3 31.2 1.0
CG B:GLU34 3.3 33.2 1.0
O B:HOH590 3.4 44.7 1.0
OD1 B:ASP60 3.5 24.7 1.0
O B:HOH570 3.7 46.8 1.0
O B:ALA30 3.8 30.9 1.0
O B:HOH544 4.0 30.6 1.0
CB B:ALA30 4.2 28.8 1.0
OE1 B:GLU34 4.2 33.1 1.0
O B:HOH526 4.2 42.1 1.0
C B:ALA30 4.4 30.9 1.0
O B:HOH549 4.5 47.4 1.0
CB B:ASP60 4.7 24.9 1.0
CA B:ALA30 4.7 31.6 1.0
CB B:GLU34 4.7 32.8 1.0

Magnesium binding site 4 out of 4 in 2yxh

Go back to Magnesium Binding Sites List in 2yxh
Magnesium binding site 4 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


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 Mazg-Related Protein From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:35.6
occ:1.00
OE1 B:GLU37 1.7 50.6 1.0
OD2 B:ASP56 1.9 24.6 1.0
OE1 B:GLU53 2.2 34.7 1.0
OE1 B:GLU34 2.3 33.1 1.0
O B:HOH544 2.3 30.6 1.0
O B:HOH532 2.5 37.7 1.0
CD B:GLU37 2.7 41.5 1.0
OE2 B:GLU37 3.1 52.3 1.0
CG B:ASP56 3.1 33.5 1.0
CD B:GLU53 3.1 40.9 1.0
CD B:GLU34 3.2 35.2 1.0
OE2 B:GLU53 3.3 38.8 1.0
OE2 B:GLU34 3.4 31.1 1.0
CB B:ASP56 3.6 29.7 1.0
O B:HOH604 4.0 52.3 1.0
O A:HOH528 4.0 39.8 1.0
O B:HOH590 4.0 44.7 1.0
CG B:GLU37 4.0 40.8 1.0
CB B:GLU37 4.1 38.5 1.0
OD1 B:ASP56 4.2 18.7 1.0
CG B:GLU53 4.5 30.9 1.0
O B:HOH588 4.5 45.5 1.0
CG B:GLU34 4.6 33.2 1.0
NZ A:LYS86 4.7 34.3 1.0
CA B:GLU53 4.7 29.6 1.0
OE2 B:GLU52 4.8 41.5 1.0
CB B:GLU34 4.8 32.8 1.0
CB B:GLU53 4.8 30.2 1.0
CA B:GLU34 4.9 34.7 1.0

Reference:

B.Padmanabhan, Y.Bessho, S.Yokoyama. Crystal Structure of Mazg-Related Protein From Thermotoga Maritima To Be Published.
Page generated: Wed Aug 14 07:41:48 2024

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