Atomistry » Iron » PDB 7dya-7ek4 » 7dyb
Atomistry »
  Iron »
    PDB 7dya-7ek4 »
      7dyb »

Iron in PDB 7dyb: Thermotoga Maritima Ferritin Mutant-Flal-L

Enzymatic activity of Thermotoga Maritima Ferritin Mutant-Flal-L

All present enzymatic activity of Thermotoga Maritima Ferritin Mutant-Flal-L:
1.16.3.2;

Protein crystallography data

The structure of Thermotoga Maritima Ferritin Mutant-Flal-L, PDB code: 7dyb was solved by G.Zhao, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.32 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.343, 54.647, 59.91, 90, 109.94, 90
R / Rfree (%) 19.4 / 23.5

Iron Binding Sites:

The binding sites of Iron atom in the Thermotoga Maritima Ferritin Mutant-Flal-L (pdb code 7dyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Thermotoga Maritima Ferritin Mutant-Flal-L, PDB code: 7dyb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 1 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:24.4
occ:0.70
 OE1 H:GLU19 2.0 28.4 1.0
O H:HOH337 2.1 25.8 1.0
O H:HOH361 2.1 32.4 1.0
ND1 H:HIS55 2.1 22.4 1.0
OE1 H:GLU52 2.2 24.4 1.0
O H:HOH359 2.7 31.2 1.0
CE1 H:HIS55 3.0 22.6 1.0
CD H:GLU19 3.1 27.4 1.0
CG H:HIS55 3.2 21.8 1.0
CD H:GLU52 3.3 20.6 1.0
FE H:FE202 3.4 26.2 0.6
OE2 H:GLU19 3.5 33.7 1.0
CB H:HIS55 3.6 20.8 1.0
OE2 H:GLU52 3.7 22.7 1.0
NE2 H:HIS55 4.2 22.9 1.0
CD2 H:HIS55 4.3 23.0 1.0
OE1 H:GLN129 4.3 23.7 1.0
O H:HOH354 4.3 30.6 1.0
CG H:GLU19 4.4 26.5 1.0
OE2 H:GLU132 4.5 25.6 1.0
CG H:GLU52 4.5 17.7 1.0
CA H:GLU52 4.6 19.6 1.0
CB H:GLU52 4.7 19.4 1.0
CB H:GLU19 4.7 20.1 1.0
CG1 H:VAL99 4.8 22.2 1.0
OE1 H:GLU132 4.8 26.9 1.0

Iron binding site 2 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 2 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe202

b:26.2
occ:0.64
 O H:HOH337 2.1 25.8 1.0
OE2 H:GLU96 2.1 27.2 1.0
OE2 H:GLU52 2.2 22.7 1.0
OE1 H:GLU132 2.3 26.9 1.0
OE1 H:GLU96 2.4 24.1 1.0
CD H:GLU96 2.6 25.8 1.0
O H:HOH359 2.7 31.2 1.0
CD H:GLU52 3.0 20.6 1.0
OE1 H:GLU52 3.1 24.4 1.0
CD H:GLU132 3.3 25.2 1.0
FE H:FE201 3.4 24.4 0.7
OE2 H:GLU132 3.6 25.6 1.0
CG H:GLU96 4.1 23.1 1.0
OE1 H:GLN129 4.1 23.7 1.0
NE2 H:GLN48 4.2 24.2 1.0
CE2 H:TYR26 4.3 24.4 1.0
CG H:GLU52 4.4 17.7 1.0
O H:HOH413 4.4 29.3 1.0
OH H:TYR26 4.5 27.8 1.0
O H:HOH361 4.6 32.4 1.0
CE1 H:HIS55 4.6 22.6 1.0
CG H:GLU132 4.6 27.2 1.0
NE2 H:GLN129 4.7 21.0 1.0
ND1 H:HIS55 4.7 22.4 1.0
CD H:GLN129 4.8 20.3 1.0
CB H:GLU132 4.9 25.0 1.0
CZ H:TYR26 4.9 26.0 1.0

Iron binding site 3 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 3 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:29.1
occ:0.67
 OE2 A:GLU19 2.0 29.3 1.0
O A:HOH332 2.0 23.7 1.0
OE1 A:GLU52 2.1 23.7 1.0
CD2 A:HIS55 2.2 19.9 1.0
CD A:GLU19 3.0 29.9 1.0
CG A:HIS55 3.2 23.0 1.0
FE A:FE202 3.2 23.6 0.6
CD A:GLU52 3.2 24.5 1.0
O A:HOH389 3.3 32.4 1.0
NE2 A:HIS55 3.3 24.5 1.0
OE1 A:GLU19 3.3 37.4 1.0
CB A:HIS55 3.6 24.2 1.0
OE2 A:GLU52 3.7 24.7 1.0
OE1 A:GLN129 4.2 22.7 1.0
CG A:GLU19 4.3 25.4 1.0
ND1 A:HIS55 4.3 27.4 1.0
CE1 A:HIS55 4.4 24.2 1.0
CG A:GLU52 4.5 19.9 1.0
OE2 A:GLU132 4.5 38.4 1.0
CA A:GLU52 4.5 21.6 1.0
O A:HOH339 4.5 31.6 1.0
CB A:GLU19 4.6 21.4 1.0
OE1 A:GLU132 4.6 32.2 1.0
CB A:GLU52 4.7 21.0 1.0
CG1 A:VAL99 4.7 20.4 1.0
CD A:GLU132 4.9 30.7 1.0
OE1 A:GLU96 4.9 24.3 1.0
O A:GLU52 5.0 21.8 1.0

Iron binding site 4 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 4 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:23.6
occ:0.58
 O A:HOH332 2.0 23.7 1.0
OE2 A:GLU96 2.2 29.6 1.0
OE2 A:GLU52 2.2 24.7 1.0
OE1 A:GLU132 2.3 32.2 1.0
O A:HOH389 2.4 32.4 1.0
OE1 A:GLU96 2.5 24.3 1.0
CD A:GLU96 2.6 28.2 1.0
CD A:GLU52 2.9 24.5 1.0
OE1 A:GLU52 3.0 23.7 1.0
FE A:FE201 3.2 29.1 0.7
CD A:GLU132 3.3 30.7 1.0
OE2 A:GLU132 3.7 38.4 1.0
NE2 A:GLN48 4.1 24.3 1.0
OE1 A:GLN129 4.1 22.7 1.0
CG A:GLU96 4.1 24.6 1.0
CG A:GLU52 4.3 19.9 1.0
OH A:TYR26 4.4 29.6 1.0
CE2 A:TYR26 4.4 25.4 1.0
CD2 A:HIS55 4.4 19.9 1.0
CG A:GLU132 4.5 33.5 1.0
NE2 A:HIS55 4.6 24.5 1.0
CB A:GLU132 4.6 28.5 1.0
NE2 A:GLN129 4.7 19.7 1.0
OE2 A:GLU19 4.8 29.3 1.0
CD A:GLN129 4.9 24.6 1.0
CZ A:TYR26 4.9 29.0 1.0

Iron binding site 5 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 5 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:25.1
occ:0.78
 O B:HOH334 2.0 29.6 1.0
OE1 B:GLU52 2.1 27.6 1.0
OE1 B:GLU19 2.1 27.6 1.0
O B:HOH341 2.2 30.6 1.0
ND1 B:HIS55 2.2 24.3 1.0
O B:HOH398 2.9 36.7 1.0
CE1 B:HIS55 3.1 24.5 1.0
CD B:GLU19 3.2 26.2 1.0
CD B:GLU52 3.2 27.0 1.0
FE B:FE202 3.2 28.4 0.5
CG B:HIS55 3.3 24.7 1.0
OE2 B:GLU19 3.5 34.2 1.0
OE2 B:GLU52 3.6 28.6 1.0
CB B:HIS55 3.7 21.9 1.0
OE1 B:GLN129 4.1 29.1 1.0
NE2 B:HIS55 4.3 28.5 1.0
CD2 B:HIS55 4.4 24.1 1.0
CG B:GLU19 4.5 25.9 1.0
CG B:GLU52 4.5 18.9 1.0
CA B:GLU52 4.5 22.4 1.0
CB B:GLU52 4.6 20.1 1.0
OE1 B:GLU132 4.6 34.5 1.0
CG1 B:VAL99 4.8 24.0 1.0
CB B:GLU19 4.8 18.5 1.0
OE1 B:GLU96 5.0 27.8 1.0
CD B:GLU132 5.0 31.7 1.0

Iron binding site 6 out of 6 in 7dyb

Go back to Iron Binding Sites List in 7dyb
Iron binding site 6 out of 6 in the Thermotoga Maritima Ferritin Mutant-Flal-L


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Thermotoga Maritima Ferritin Mutant-Flal-L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:28.4
occ:0.53
 O B:HOH334 1.8 29.6 1.0
OE2 B:GLU52 2.2 28.6 1.0
OE2 B:GLU96 2.3 34.5 1.0
OE1 B:GLU132 2.4 34.5 1.0
OE1 B:GLU96 2.5 27.8 1.0
O B:HOH398 2.6 36.7 1.0
CD B:GLU96 2.7 28.1 1.0
CD B:GLU52 2.9 27.0 1.0
OE1 B:GLU52 3.0 27.6 1.0
FE B:FE201 3.2 25.1 0.8
CD B:GLU132 3.4 31.7 1.0
OE1 B:GLN129 4.0 29.1 1.0
NE2 B:GLN48 4.1 24.5 1.0
CG B:GLU96 4.1 27.9 1.0
OE2 B:GLU132 4.2 40.1 1.0
CG B:GLU132 4.3 32.0 1.0
OH B:TYR26 4.3 33.0 1.0
CE2 B:TYR26 4.3 25.1 1.0
CG B:GLU52 4.4 18.9 1.0
O B:HOH341 4.4 30.6 1.0
CB B:GLU132 4.4 29.6 1.0
CE1 B:HIS55 4.5 24.5 1.0
ND1 B:HIS55 4.5 24.3 1.0
NE2 B:GLN129 4.6 24.3 1.0
CD B:GLN129 4.8 28.4 1.0
CZ B:TYR26 4.8 26.8 1.0
OE1 B:GLU19 5.0 27.6 1.0

Reference:

X.Zhang, Y.Liu, B.Zheng, J.Zang, C.Lv, T.Zhang, H.Wang, G.Zhao. Protein Interface Redesign Facilitates the Transformation of Nanocage Building Blocks to 1D and 2D Nanomaterials. Nat Commun V. 12 4849 2021.
ISSN: ESSN 2041-1723
PubMed: 34381032
DOI: 10.1038/S41467-021-25199-X
Page generated: Thu Aug 8 04:36:43 2024

Last articles

Ca in 5VE9
Ca in 5VEP
Ca in 5V9U
Ca in 5VCO
Ca in 5VCN
Ca in 5VC1
Ca in 5VA9
Ca in 5VBJ
Ca in 5VAO
Ca in 5V8K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy