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Magnesium in PDB 4h1z: Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)

Protein crystallography data

The structure of Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104), PDB code: 4h1z 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, 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) 45.02 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.723, 121.702, 137.691, 90.00, 99.79, 90.00
R / Rfree (%) 17.2 / 22.9

Other elements in 4h1z:

The structure of Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) (pdb code 4h1z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104), PDB code: 4h1z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4h1z

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Magnesium binding site 1 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


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 Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:41.1
occ:1.00
 OE1 A:GLU267 1.9 33.6 1.0
O2 A:FMT402 2.1 60.0 1.0
OE2 A:GLU241 2.1 35.2 1.0
O A:HOH517 2.1 40.2 1.0
OD2 A:ASP215 2.2 35.8 1.0
O A:HOH519 2.4 34.5 1.0
C A:FMT402 2.8 63.9 1.0
CD A:GLU267 3.0 37.3 1.0
CD A:GLU241 3.1 47.6 1.0
CG A:ASP215 3.2 47.7 1.0
OE2 A:GLU267 3.4 37.1 1.0
OD1 A:ASP215 3.7 39.3 1.0
O A:HOH610 3.8 35.8 1.0
OE1 A:GLU241 3.8 36.9 1.0
CG A:GLU241 3.9 34.6 1.0
O1 A:FMT402 4.0 62.1 1.0
NZ A:LYS185 4.1 31.0 1.0
O A:HOH526 4.1 33.7 1.0
O A:HOH612 4.3 46.7 1.0
CD2 A:HIS316 4.3 38.3 1.0
CG A:GLU267 4.3 30.8 1.0
CB A:ASP215 4.5 28.2 1.0
NE2 A:HIS316 4.6 31.1 1.0
CH2 A:TRP218 4.7 36.6 1.0
O A:HOH561 4.7 46.2 1.0
CB A:GLU267 4.9 35.4 1.0
CE A:LYS185 5.0 30.7 1.0

Magnesium binding site 2 out of 8 in 4h1z

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Magnesium binding site 2 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


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 Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:24.9
occ:1.00
 OE2 B:GLU241 2.0 28.5 1.0
OD2 B:ASP215 2.0 24.1 1.0
O B:HOH504 2.1 25.5 1.0
O1 B:FMT403 2.1 36.2 1.0
OE1 B:GLU267 2.1 24.2 1.0
O B:HOH638 2.1 26.1 1.0
C B:FMT403 2.6 39.1 1.0
CD B:GLU241 3.1 35.7 1.0
CG B:ASP215 3.1 27.8 1.0
CD B:GLU267 3.1 42.9 1.0
OE2 B:GLU267 3.4 30.2 1.0
OD1 B:ASP215 3.5 28.1 1.0
OE1 B:GLU241 3.8 29.6 1.0
CG B:GLU241 3.9 23.0 1.0
O2 B:FMT403 3.9 39.8 1.0
O B:HOH639 4.1 32.2 1.0
O B:HOH505 4.1 21.0 1.0
O B:HOH598 4.1 39.8 1.0
NZ B:LYS185 4.2 25.9 1.0
CD2 B:HIS316 4.3 37.2 1.0
CB B:ASP215 4.3 21.7 1.0
CG B:GLU267 4.4 27.5 1.0
NE2 B:HIS316 4.4 31.5 1.0
CH2 B:TRP218 4.5 27.7 1.0
O B:HOH602 4.8 42.5 1.0
O B:HOH727 4.8 75.2 1.0
CZ2 B:TRP218 4.9 31.3 1.0
CE B:LYS185 4.9 24.8 1.0
NE2 B:HIS217 4.9 34.0 1.0

Magnesium binding site 3 out of 8 in 4h1z

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Magnesium binding site 3 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


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 Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:34.0
occ:1.00
 OD2 C:ASP215 1.9 32.3 1.0
O C:HOH635 2.1 34.9 1.0
OE1 C:GLU267 2.1 30.8 1.0
O2 C:FMT404 2.1 37.1 1.0
OE2 C:GLU241 2.1 31.1 1.0
O C:HOH504 2.2 29.7 1.0
C C:FMT404 2.7 48.6 1.0
CG C:ASP215 3.0 28.2 1.0
CD C:GLU241 3.0 34.1 1.0
CD C:GLU267 3.2 37.0 1.0
OD1 C:ASP215 3.4 30.0 1.0
OE2 C:GLU267 3.6 37.4 1.0
OE1 C:GLU241 3.7 38.7 1.0
CG C:GLU241 3.8 25.0 1.0
O1 C:FMT404 3.9 44.9 1.0
NZ C:LYS185 4.0 26.9 1.0
O C:HOH590 4.1 33.5 1.0
O C:HOH561 4.2 41.0 1.0
O C:HOH540 4.2 27.8 1.0
CB C:ASP215 4.3 25.9 1.0
CD2 C:HIS316 4.5 30.1 1.0
CG C:GLU267 4.5 38.1 1.0
CH2 C:TRP218 4.6 34.5 1.0
NE2 C:HIS316 4.8 29.4 1.0
CE C:LYS185 4.9 22.8 1.0
CZ2 C:TRP218 5.0 29.8 1.0

Magnesium binding site 4 out of 8 in 4h1z

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Magnesium binding site 4 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


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 Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:29.6
occ:1.00
 O D:HOH587 2.0 30.5 1.0
OE2 D:GLU241 2.0 33.4 1.0
OD2 D:ASP215 2.1 27.2 1.0
OE1 D:GLU267 2.1 34.4 1.0
O D:HOH586 2.2 26.1 1.0
O D:HOH515 2.2 23.3 1.0
CD D:GLU241 3.0 35.5 1.0
CD D:GLU267 3.0 37.8 1.0
CG D:ASP215 3.1 47.7 1.0
OE2 D:GLU267 3.3 45.2 1.0
OD1 D:ASP215 3.4 29.5 1.0
OE1 D:GLU241 3.8 26.2 1.0
CG D:GLU241 3.8 24.3 1.0
O D:HOH529 4.1 34.9 1.0
NZ D:LYS185 4.1 28.6 1.0
O D:HOH526 4.2 26.7 1.0
CG D:GLU267 4.4 31.8 1.0
CB D:ASP215 4.4 31.2 1.0
O D:HOH631 4.4 34.0 1.0
O D:HOH655 4.5 53.0 1.0
CD2 D:HIS316 4.5 32.5 1.0
O D:HOH501 4.5 40.2 1.0
CH2 D:TRP218 4.6 28.9 1.0
NE2 D:HIS316 4.6 33.1 1.0
CZ2 D:TRP218 4.9 28.9 1.0
CE D:LYS185 4.9 29.7 1.0
CB D:GLU267 5.0 28.5 1.0

Magnesium binding site 5 out of 8 in 4h1z

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Magnesium binding site 5 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


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 Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:27.1
occ:1.00
 O1 E:FMT402 2.0 27.3 1.0
OE2 E:GLU241 2.0 29.2 1.0
OE1 E:GLU267 2.1 28.9 1.0
OD2 E:ASP215 2.1 33.1 1.0
O E:HOH503 2.1 24.1 1.0
O E:HOH505 2.1 25.8 1.0
C E:FMT402 2.9 37.9 1.0
CD E:GLU267 3.1 34.8 1.0
CG E:ASP215 3.1 27.5 1.0
CD E:GLU241 3.1 40.0 1.0
OE2 E:GLU267 3.4 30.5 1.0
OD1 E:ASP215 3.5 28.3 1.0
CG E:GLU241 3.9 22.8 1.0
O E:HOH511 4.0 24.7 1.0
OE1 E:GLU241 4.1 34.5 1.0
O E:HOH538 4.1 30.6 1.0
O2 E:FMT402 4.1 37.5 1.0
NZ E:LYS185 4.2 32.8 1.0
CB E:ASP215 4.4 30.9 1.0
CG E:GLU267 4.4 28.1 1.0
CH2 E:TRP218 4.5 26.4 1.0
CD2 E:HIS316 4.5 41.6 1.0
O E:HOH636 4.5 35.5 1.0
NE2 E:HIS316 4.7 31.9 1.0
CZ2 E:TRP218 4.9 19.6 1.0

Magnesium binding site 6 out of 8 in 4h1z

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Magnesium binding site 6 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


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 Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:32.2
occ:1.00
 O F:HOH612 2.1 32.7 1.0
OE2 F:GLU241 2.1 27.7 1.0
O1 F:FMT402 2.1 31.2 1.0
OD2 F:ASP215 2.1 27.5 1.0
OE1 F:GLU267 2.2 26.7 1.0
O F:HOH513 2.2 30.2 1.0
C F:FMT402 2.9 43.6 1.0
CD F:GLU241 3.0 23.6 1.0
CD F:GLU267 3.1 22.2 1.0
CG F:ASP215 3.1 35.2 1.0
OE2 F:GLU267 3.3 31.8 1.0
OD1 F:ASP215 3.5 25.8 1.0
CG F:GLU241 3.8 18.0 1.0
OE1 F:GLU241 3.9 30.4 1.0
O F:HOH519 4.0 34.2 1.0
O2 F:FMT402 4.1 39.8 1.0
O F:HOH505 4.2 20.6 1.0
NZ F:LYS185 4.3 22.3 1.0
O F:HOH613 4.3 37.3 1.0
CG F:GLU267 4.4 21.2 1.0
CB F:ASP215 4.5 27.1 1.0
CD2 F:HIS316 4.5 26.5 1.0
CH2 F:TRP218 4.5 33.6 1.0
NE2 F:HIS316 4.6 28.9 1.0
CZ2 F:TRP218 4.8 28.3 1.0
O F:HOH681 4.8 43.3 1.0
O F:HOH682 4.9 55.0 1.0

Magnesium binding site 7 out of 8 in 4h1z

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Magnesium binding site 7 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg402

b:23.8
occ:1.00
 O G:HOH507 2.0 26.6 1.0
OE2 G:GLU241 2.0 27.4 1.0
O2 G:FMT403 2.1 22.4 1.0
OE1 G:GLU267 2.1 27.1 1.0
OD2 G:ASP215 2.1 22.1 1.0
O G:HOH633 2.2 22.0 1.0
C G:FMT403 3.0 38.4 1.0
CD G:GLU267 3.1 31.7 1.0
CD G:GLU241 3.1 21.9 1.0
CG G:ASP215 3.2 33.7 1.0
OE2 G:GLU267 3.4 29.2 1.0
OD1 G:ASP215 3.6 19.7 1.0
CG G:GLU241 3.9 19.0 1.0
OE1 G:GLU241 3.9 22.9 1.0
O G:HOH573 4.0 29.7 1.0
O1 G:FMT403 4.1 40.1 1.0
O G:HOH518 4.2 19.3 1.0
NZ G:LYS185 4.2 32.7 1.0
O G:HOH705 4.3 37.4 1.0
CD2 G:HIS316 4.4 33.1 1.0
CG G:GLU267 4.4 21.4 1.0
CB G:ASP215 4.5 27.1 1.0
NE2 G:HIS316 4.5 32.8 1.0
CH2 G:TRP218 4.6 23.3 1.0
O G:HOH587 4.8 41.7 1.0
CZ2 G:TRP218 4.9 27.8 1.0
CE G:LYS185 4.9 26.6 1.0

Magnesium binding site 8 out of 8 in 4h1z

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Magnesium binding site 8 out of 8 in the Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Putative Isomerase From Sinorhizobium Meliloti, Open Loop Conformation (Target Efi-502104) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:37.5
occ:1.00
 OD2 H:ASP215 1.9 31.1 1.0
OE1 H:GLU267 2.0 33.1 1.0
O H:HOH576 2.1 31.7 1.0
O H:HOH615 2.2 33.1 1.0
OE2 H:GLU241 2.2 35.5 1.0
O2 H:FMT402 2.2 34.9 1.0
CG H:ASP215 2.9 28.5 1.0
CD H:GLU267 3.0 38.8 1.0
C H:FMT402 3.1 65.5 1.0
CD H:GLU241 3.1 34.2 1.0
OD1 H:ASP215 3.3 31.9 1.0
OE2 H:GLU267 3.4 36.5 1.0
CG H:GLU241 3.7 25.7 1.0
OE1 H:GLU241 4.0 37.5 1.0
O H:HOH510 4.0 29.5 1.0
NZ H:LYS185 4.0 38.7 1.0
O H:HOH548 4.2 40.1 1.0
CB H:ASP215 4.2 32.7 1.0
O1 H:FMT402 4.2 48.2 1.0
CG H:GLU267 4.2 22.5 1.0
CH2 H:TRP218 4.4 34.5 1.0
O H:HOH640 4.6 44.6 1.0
CD2 H:HIS316 4.6 30.5 1.0
NE2 H:HIS316 4.8 36.5 1.0
CZ2 H:TRP218 4.8 32.5 1.0
CE H:LYS185 4.8 36.6 1.0

Reference:

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, J.A.Gerlt, S.C.Almo. Crystal Structure of Enolase Q92ZS5 (Target Efi-502104) From Sinorhizobium Meliloti To Be Published.
Page generated: Fri Aug 16 16:08:35 2024

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