Atomistry » Magnesium » PDB 4gyi-4h99 » 4h1z
Atomistry »
  Magnesium »
    PDB 4gyi-4h99 »
      4h1z »

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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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

Go back to Magnesium Binding Sites List in 4h1z
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: Mon Dec 14 17:06:56 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy