Atomistry » Cobalt » PDB 6vyh-7cel » 7b1v
Atomistry »
  Cobalt »
    PDB 6vyh-7cel »
      7b1v »

Cobalt in PDB 7b1v: Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt

Protein crystallography data

The structure of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt, PDB code: 7b1v was solved by D.Maurer, F.J.Marcos-Torres, J.J.Griese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.10 / 2.04
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.888, 45.564, 66.275, 109.12, 93.2, 113.98
R / Rfree (%) 21.8 / 25.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt (pdb code 7b1v). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt, PDB code: 7b1v:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 7b1v

Go back to Cobalt Binding Sites List in 7b1v
Cobalt binding site 1 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co301

b:18.9
occ:1.00
OE2 A:GLU105 1.9 18.6 1.0
O A:HOH406 2.0 22.9 1.0
O A:CSD102 2.0 19.0 1.0
OD1 A:CSD102 2.1 21.2 1.0
NE2 A:HIS106 2.2 20.6 1.0
SD A:MET10 2.5 25.3 1.0
C A:CSD102 3.0 19.9 1.0
CD A:GLU105 3.0 18.9 1.0
CD2 A:HIS106 3.1 20.8 1.0
CE1 A:HIS106 3.2 20.7 1.0
SG A:CSD102 3.4 22.3 1.0
CA A:CSD102 3.5 20.2 1.0
CE A:MET10 3.5 25.7 1.0
CG A:MET10 3.5 26.7 1.0
CG A:GLU105 3.6 19.0 1.0
CB A:CSD102 3.8 20.8 1.0
OD2 A:CSD102 3.9 21.6 1.0
OE1 A:GLU105 4.1 19.2 1.0
O A:LEU4 4.1 29.3 1.0
CG A:HIS106 4.2 20.7 1.0
N A:ARG103 4.2 19.4 1.0
ND1 A:HIS106 4.3 20.5 1.0
NH1 A:ARG13 4.4 29.5 1.0
CA A:ARG103 4.7 19.5 1.0
N A:CSD102 4.8 19.7 1.0
CB A:MET10 4.9 27.2 1.0
O A:ALA101 5.0 19.9 1.0

Cobalt binding site 2 out of 4 in 7b1v

Go back to Cobalt Binding Sites List in 7b1v
Cobalt binding site 2 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co302

b:23.0
occ:1.00
OE1 A:GLU172 1.8 23.0 1.0
OE2 A:GLU83 1.9 23.1 1.0
NE2 A:HIS79 2.1 17.8 1.0
ND1 A:HIS98 2.1 23.8 1.0
OE1 A:GLN175 2.3 22.8 1.0
CD A:GLU83 2.9 23.4 1.0
CD A:GLU172 2.9 24.4 1.0
CE1 A:HIS98 3.0 24.0 1.0
CE1 A:HIS79 3.0 17.8 1.0
CD2 A:HIS79 3.1 18.0 1.0
CG A:HIS98 3.2 24.1 1.0
OE1 A:GLU83 3.3 24.1 1.0
CD A:GLN175 3.3 23.0 1.0
OE2 A:GLU172 3.4 24.4 1.0
CB A:HIS98 3.6 24.5 1.0
O A:HOH404 3.7 26.0 1.0
NE2 A:GLN175 3.9 22.6 1.0
CA A:HIS98 4.1 25.1 1.0
CG A:GLU83 4.2 23.6 1.0
ND1 A:HIS79 4.2 17.8 1.0
NE2 A:HIS98 4.2 23.8 1.0
CG A:GLU172 4.2 25.0 1.0
CG A:HIS79 4.2 18.1 1.0
CD2 A:HIS98 4.3 23.8 1.0
CB A:GLN175 4.5 24.6 1.0
CG A:GLN175 4.5 23.9 1.0
CB A:GLU172 4.5 25.8 1.0
CA A:GLU172 4.6 26.3 1.0
CD2 A:TYR128 4.6 33.8 1.0
CE2 A:TYR128 4.7 35.0 1.0
O A:HIS98 4.8 25.0 1.0
C A:HIS98 4.9 25.0 1.0

Cobalt binding site 3 out of 4 in 7b1v

Go back to Cobalt Binding Sites List in 7b1v
Cobalt binding site 3 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:20.3
occ:1.00
OE2 B:GLU105 1.9 18.5 1.0
O B:CSD102 2.1 21.6 1.0
NE2 B:HIS106 2.1 21.4 1.0
OD1 B:CSD102 2.1 23.1 1.0
O B:HOH422 2.1 28.0 1.0
SD B:MET10 2.5 28.0 1.0
CD B:GLU105 3.0 18.7 1.0
CE1 B:HIS106 3.0 21.9 1.0
CD2 B:HIS106 3.1 21.4 1.0
C B:CSD102 3.1 21.1 1.0
SG B:CSD102 3.5 23.8 1.0
CG B:GLU105 3.5 19.0 1.0
CG B:MET10 3.5 28.3 1.0
CE B:MET10 3.6 28.6 1.0
CA B:CSD102 3.6 21.2 1.0
CB B:CSD102 3.9 22.3 1.0
OE1 B:GLU105 4.1 18.8 1.0
OD2 B:CSD102 4.1 23.9 1.0
ND1 B:HIS106 4.1 21.6 1.0
O B:LEU4 4.2 34.1 1.0
CG B:HIS106 4.2 21.5 1.0
NH1 B:ARG13 4.2 26.4 1.0
N B:ARG103 4.3 20.7 1.0
CA B:ARG103 4.7 20.5 1.0
N B:CSD102 4.9 20.3 1.0
CB B:MET10 5.0 28.4 1.0
O B:ALA101 5.0 19.3 1.0

Cobalt binding site 4 out of 4 in 7b1v

Go back to Cobalt Binding Sites List in 7b1v
Cobalt binding site 4 out of 4 in the Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Dtxr-Like Iron-Dependent Regulator Ider Complexed with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co302

b:22.1
occ:1.00
OE2 B:GLU83 1.9 22.9 1.0
ND1 B:HIS98 2.0 22.9 1.0
OE1 B:GLU172 2.0 26.4 1.0
NE2 B:HIS79 2.1 19.0 1.0
OE1 B:GLN175 2.2 23.7 1.0
CE1 B:HIS98 2.8 23.0 1.0
CD B:GLU83 2.9 23.3 1.0
CG B:HIS98 3.1 23.7 1.0
CE1 B:HIS79 3.1 19.2 1.0
CD B:GLU172 3.1 28.0 1.0
CD2 B:HIS79 3.1 19.4 1.0
CD B:GLN175 3.2 24.6 1.0
OE1 B:GLU83 3.3 23.0 1.0
O B:HOH404 3.5 21.6 1.0
CB B:HIS98 3.6 23.7 1.0
OE2 B:GLU172 3.6 28.9 1.0
NE2 B:GLN175 3.8 24.3 1.0
NE2 B:HIS98 4.0 23.5 1.0
CA B:HIS98 4.0 24.0 1.0
CD2 B:HIS98 4.1 23.8 1.0
CG B:GLU83 4.2 23.7 1.0
ND1 B:HIS79 4.2 19.4 1.0
CG B:HIS79 4.3 19.4 1.0
CG B:GLU172 4.4 27.9 1.0
CG B:GLN175 4.4 25.8 1.0
CB B:GLN175 4.4 27.0 1.0
CB B:GLU172 4.6 28.1 1.0
CD2 B:TYR128 4.6 27.5 1.0
CE2 B:TYR128 4.7 27.3 1.0
CA B:GLU172 4.7 28.7 1.0
O B:HIS98 4.7 24.4 1.0
C B:HIS98 4.9 24.5 1.0

Reference:

F.J.Marcos-Torres, D.Maurer, J.J.Griese. The Bacterial Iron Sensor Ider Recognizes Its Dna Targets By Indirect Readout Biorxiv 2021.
DOI: 10.1101/2021.02.12.430932
Page generated: Sat Apr 3 14:48:43 2021

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