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Zinc in PDB 5wpn: Zn-Bound Structure of Chaetopterus Variopedatus Ferritin

Enzymatic activity of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin

All present enzymatic activity of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin, PDB code: 5wpn was solved by E.De Meulenaere, J.B.Bailey, F.A.Tezcan, D.Deheyn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.47 / 1.57
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.870, 181.870, 181.870, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.3

Other elements in 5wpn:

The structure of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin (pdb code 5wpn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin, PDB code: 5wpn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 5wpn

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Zinc binding site 1 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:12.1
occ:0.87
 O A:HOH325 2.0 18.6 1.0
OE1 A:GLU24 2.0 13.7 1.0
OE2 A:GLU59 2.1 15.2 1.0
ND1 A:HIS62 2.1 17.5 1.0
O A:HOH335 2.2 17.8 1.0
CD A:GLU24 3.0 15.8 1.0
CE1 A:HIS62 3.0 20.9 1.0
CD A:GLU59 3.1 18.2 1.0
HE1 A:HIS62 3.1 25.1 1.0
CG A:HIS62 3.2 15.0 1.0
HG11 A:VAL107 3.3 22.1 1.0
OE2 A:GLU24 3.3 15.8 1.0
HB2 A:HIS62 3.4 14.7 1.0
ZN A:ZN203 3.4 14.7 0.8
HB3 A:HIS62 3.5 14.7 1.0
OE1 A:GLU59 3.5 18.5 1.0
HA A:GLU59 3.5 11.4 1.0
CB A:HIS62 3.6 12.3 1.0
OE1 A:GLN138 3.8 30.7 1.0
O A:HOH346 4.1 33.4 1.0
NE2 A:HIS62 4.1 21.1 1.0
CG1 A:VAL107 4.2 18.4 1.0
CD2 A:HIS62 4.2 21.2 1.0
HB3 A:GLU24 4.2 15.3 1.0
CG A:GLU24 4.3 11.7 1.0
HA A:GLU24 4.3 13.3 1.0
CG A:GLU59 4.4 14.0 1.0
HB3 A:GLU59 4.4 14.3 1.0
CA A:GLU59 4.4 9.5 1.0
O A:HOH472 4.5 24.4 1.0
HG12 A:VAL107 4.5 22.1 1.0
HG13 A:VAL107 4.5 22.1 1.0
HE2 A:TYR134 4.6 16.0 1.0
CB A:GLU59 4.7 11.9 1.0
HG3 A:GLU24 4.7 14.1 1.0
HG21 A:VAL107 4.7 19.5 1.0
CB A:GLU24 4.7 12.8 1.0
O A:HOH453 4.8 42.4 1.0
HD2 A:TYR134 4.8 16.1 1.0
CD A:GLN138 4.9 23.2 1.0
HD11 A:LEU111 4.9 20.2 1.0
HB3 A:ALA27 4.9 14.8 1.0
HG2 A:GLU59 4.9 16.8 1.0
OE2 A:GLU104 4.9 19.3 1.0
HG3 A:GLU59 4.9 16.8 1.0
HG2 A:GLU24 4.9 14.1 1.0

Zinc binding site 2 out of 12 in 5wpn

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Zinc binding site 2 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:18.1
occ:0.48
 HZ1 A:LYS53 1.4 57.4 1.0
HZ2 A:LYS53 1.7 57.4 1.0
NZ A:LYS53 1.9 47.8 1.0
O A:HOH491 2.1 24.9 1.0
NE2 A:HIS49 2.2 16.9 1.0
O A:HOH500 2.3 31.6 1.0
HZ3 A:LYS53 2.6 57.4 1.0
HE3 A:LYS53 2.8 59.8 1.0
CE A:LYS53 2.9 49.8 1.0
CD2 A:HIS49 3.0 17.0 1.0
HD2 A:HIS49 3.0 20.4 1.0
CE1 A:HIS49 3.3 13.6 1.0
HE2 A:LYS53 3.5 59.8 1.0
HE1 A:HIS49 3.6 16.4 1.0
HH2 A:TRP36 3.8 16.2 1.0
O A:HOH555 4.0 41.0 1.0
HD2 A:LYS53 4.1 47.8 1.0
CD A:LYS53 4.1 39.8 1.0
CH2 A:TRP36 4.2 13.5 1.0
CG A:HIS49 4.2 14.1 1.0
ND1 A:HIS49 4.3 11.2 1.0
O A:HOH411 4.3 23.3 1.0
HD3 A:LYS53 4.4 47.8 1.0
HG2 A:LYS50 4.4 28.4 1.0
O A:HOH339 4.7 28.9 1.0
CZ2 A:TRP36 4.7 14.8 1.0
HZ2 A:TRP36 4.7 17.8 1.0
CZ3 A:TRP36 4.8 14.1 1.0
HZ3 A:TRP36 4.8 16.9 1.0

Zinc binding site 3 out of 12 in 5wpn

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Zinc binding site 3 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:14.7
occ:0.79
 O A:HOH325 1.9 18.6 1.0
OE1 A:GLU59 1.9 18.5 1.0
O A:HOH472 2.1 24.4 1.0
OE2 A:GLU104 2.2 19.3 1.0
OE1 A:GLU104 2.3 23.2 1.0
CD A:GLU104 2.5 18.2 1.0
CD A:GLU59 2.9 18.2 1.0
OE2 A:GLU59 3.2 15.2 1.0
ZN A:ZN201 3.4 12.1 0.9
HE22 A:GLN138 3.5 26.2 1.0
HE1 A:HIS62 3.5 25.1 1.0
OE1 A:GLN138 3.7 30.7 1.0
O A:HOH317 3.7 28.7 1.0
HG A:SER141 3.7 21.0 0.5
HE2 A:TYR31 3.7 16.4 1.0
HH A:TYR31 4.0 35.8 1.0
CG A:GLU104 4.0 12.5 1.0
O A:HOH453 4.1 42.4 1.0
HG A:SER141 4.2 24.0 0.5
NE2 A:GLN138 4.2 21.8 1.0
CE1 A:HIS62 4.2 20.9 1.0
HG11 A:VAL107 4.2 22.1 1.0
CG A:GLU59 4.2 14.0 1.0
CD A:GLN138 4.3 23.2 1.0
HA A:GLU104 4.4 14.1 1.0
ND1 A:HIS62 4.4 17.5 1.0
HG2 A:GLU59 4.4 16.8 1.0
HG3 A:GLU104 4.4 15.0 1.0
HG21 A:VAL107 4.4 19.5 1.0
HG2 A:GLU104 4.5 15.0 1.0
HG3 A:GLU59 4.5 16.8 1.0
OG A:SER141 4.5 17.5 0.5
CE2 A:TYR31 4.6 13.6 1.0
O A:HOH335 4.7 17.8 1.0
HB3 A:GLU104 4.7 16.2 1.0
HB A:VAL107 4.7 16.4 1.0
HB3 A:SER141 4.8 19.9 0.5
HB1 A:ALA27 4.8 14.8 1.0
OH A:TYR31 4.8 29.9 1.0
CB A:GLU104 4.9 13.5 1.0
OG A:SER141 5.0 20.0 0.5
HB2 A:SER141 5.0 19.9 0.5
HE21 A:GLN138 5.0 26.2 1.0
HB3 A:SER141 5.0 19.4 0.5
HB2 A:SER141 5.0 19.4 0.5

Zinc binding site 4 out of 12 in 5wpn

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Zinc binding site 4 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:21.8
occ:0.76
 NE2 A:HIS121 1.9 23.7 1.0
OD2 A:ASP12 1.9 26.5 1.0
O A:HOH469 2.2 35.9 1.0
O A:HOH505 2.3 27.9 1.0
O A:HOH462 2.3 35.7 1.0
CG A:ASP12 2.8 24.3 1.0
CE1 A:HIS121 2.8 25.5 1.0
HE1 A:HIS121 2.9 30.6 1.0
CD2 A:HIS121 3.0 18.5 1.0
OD1 A:ASP12 3.0 27.8 1.0
HD2 A:HIS121 3.2 22.2 1.0
HG13 A:VAL117 3.6 26.4 1.0
O A:HOH338 3.9 43.5 1.0
ND1 A:HIS121 3.9 28.2 1.0
O A:HOH429 4.0 28.3 1.0
CG A:HIS121 4.0 23.0 1.0
CB A:ASP12 4.1 20.0 1.0
O A:HOH340 4.1 27.0 1.0
HB3 A:ASP12 4.3 24.1 1.0
HB2 A:ASP12 4.4 24.1 1.0
CG1 A:VAL117 4.4 22.0 1.0
HG12 A:VAL117 4.5 26.4 1.0
HB1 A:ALA10 4.5 20.0 1.0
HD1 A:HIS121 4.7 33.8 1.0
HG11 A:VAL117 4.7 26.4 1.0
O A:HOH534 4.7 48.5 1.0
H A:ASP12 4.8 16.6 1.0
O A:HOH518 4.9 50.9 1.0

Zinc binding site 5 out of 12 in 5wpn

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Zinc binding site 5 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:11.4
occ:0.82
 NE2 A:HIS115 2.0 13.9 1.0
O A:HOH444 2.0 17.5 1.0
CL A:CL214 2.2 26.5 1.0
SG A:CYS127 2.3 13.9 1.0
CE1 A:HIS115 3.0 14.9 1.0
CD2 A:HIS115 3.1 12.5 1.0
HB2 A:CYS127 3.1 17.6 1.0
HE1 A:HIS115 3.2 17.9 1.0
HD2 A:HIS115 3.3 15.0 1.0
CB A:CYS127 3.3 14.7 1.0
ZN A:ZN206 3.4 11.6 0.8
OE2 A:GLU131 3.7 13.6 1.0
O A:HOH584 3.7 19.6 0.3
HB3 A:CYS127 4.0 17.6 1.0
O A:HOH489 4.1 16.9 0.3
HA A:CYS127 4.1 13.4 1.0
ND1 A:HIS115 4.1 12.7 1.0
CG A:HIS115 4.2 11.3 1.0
HB2 A:ALA119 4.2 28.7 1.0
CA A:CYS127 4.3 11.2 1.0
O A:HOH473 4.4 26.7 1.0
CD A:GLU131 4.5 11.6 1.0
O A:HOH524 4.6 18.1 1.0
HG3 A:GLU131 4.7 16.1 1.0
HD1 A:HIS115 4.9 15.2 1.0
C A:CYS127 5.0 13.6 1.0

Zinc binding site 6 out of 12 in 5wpn

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Zinc binding site 6 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:11.6
occ:0.81
 O A:HOH444 1.8 17.5 1.0
OE2 A:GLU131 1.9 13.6 1.0
O A:HOH489 2.0 16.9 0.3
CD A:GLU131 2.9 11.6 1.0
OE1 A:GLU131 3.2 15.0 1.0
ZN A:ZN205 3.4 11.4 0.8
SG A:CYS127 3.6 13.9 1.0
O A:HOH584 4.0 19.6 0.3
CG A:GLU131 4.2 13.4 1.0
HG3 A:GLU131 4.4 16.1 1.0
HG2 A:GLU131 4.4 16.1 1.0
NE2 A:HIS115 4.8 13.9 1.0
ZN A:ZN207 4.8 14.7 0.2

Zinc binding site 7 out of 12 in 5wpn

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Zinc binding site 7 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:14.7
occ:0.21
 O A:HOH345 2.3 16.6 1.0
OE1 A:GLU131 2.3 15.0 1.0
CD A:GLU131 3.6 11.6 1.0
HB2 A:GLU131 3.8 17.6 1.0
O A:HOH489 3.9 16.9 0.3
HB3 A:GLU131 3.9 17.6 1.0
HA A:ASP128 4.0 17.1 1.0
CB A:GLU131 4.2 14.7 1.0
OE1 A:GLU132 4.4 15.8 0.5
OE2 A:GLU131 4.5 13.6 1.0
CG A:GLU131 4.5 13.4 1.0
OD1 A:ASP128 4.6 15.6 1.0
ZN A:ZN206 4.8 11.6 0.8
HB2 A:ASP128 5.0 17.5 1.0
CA A:ASP128 5.0 14.2 1.0

Zinc binding site 8 out of 12 in 5wpn

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Zinc binding site 8 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:19.3
occ:0.33
 O A:HOH454 1.8 28.6 1.0
NE2 A:HIS133 2.0 20.8 1.0
O A:HOH519 2.2 45.4 1.0
O A:HOH521 2.2 31.1 1.0
CE1 A:HIS133 2.8 27.2 1.0
HE1 A:HIS133 2.8 32.7 1.0
CD2 A:HIS133 3.2 18.2 1.0
HG2 A:GLU132 3.5 24.6 0.5
HD2 A:HIS133 3.5 21.9 1.0
O A:HOH367 3.9 27.2 1.0
ND1 A:HIS133 4.0 24.8 1.0
CG A:HIS133 4.2 20.9 1.0
HG3 A:GLU132 4.2 24.6 0.5
CG A:GLU132 4.3 20.5 0.5
HD1 A:PHE129 4.3 16.9 1.0
O A:HOH440 4.5 32.0 1.0
HB3 A:GLU132 4.7 26.5 0.5
HD1 A:HIS133 4.7 29.8 1.0
HB3 A:GLU132 4.7 26.3 0.5
HB2 A:GLU132 4.7 26.3 0.5
HZ3 A:LYS72 4.9 24.2 1.0
HE1 A:PHE129 5.0 15.8 1.0

Zinc binding site 9 out of 12 in 5wpn

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Zinc binding site 9 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:13.1
occ:0.15
 O A:HOH306 0.8 23.6 0.6
O A:HOH360 1.8 25.7 0.2
OE2 A:GLU167 1.9 28.8 1.0
CD A:GLU167 3.1 25.4 1.0
HE1 A:MET163 3.3 20.1 1.0
O A:HOH314 3.7 36.3 1.0
OE1 A:GLU167 3.7 28.1 1.0
CE A:MET163 4.1 16.8 1.0
HG2 A:GLU167 4.1 17.3 1.0
HE3 A:MET163 4.1 20.1 1.0
CG A:GLU167 4.2 14.4 1.0
HE2 A:MET163 4.3 20.1 1.0
HG3 A:GLU167 4.5 17.3 1.0
HB3 A:LYS166 4.5 17.6 1.0

Zinc binding site 10 out of 12 in 5wpn

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Zinc binding site 10 out of 12 in the Zn-Bound Structure of Chaetopterus Variopedatus Ferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Zn-Bound Structure of Chaetopterus Variopedatus Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:32.1
occ:0.45
 O A:HOH303 1.8 41.2 1.0
O A:HOH304 2.4 35.1 1.0
NE2 A:HIS54 2.6 43.1 1.0
HE22 A:GLN55 2.7 61.3 1.0
HD2 A:HIS54 3.1 54.4 1.0
CD2 A:HIS54 3.2 45.4 1.0
NE2 A:GLN55 3.5 51.1 1.0
HE21 A:GLN55 3.7 61.3 1.0
OE1 A:GLU58 3.7 32.5 0.4
OE2 A:GLU58 3.7 39.2 0.4
CE1 A:HIS54 3.7 41.6 1.0
OE1 A:GLU58 3.9 42.7 0.4
CD A:GLU58 4.0 32.6 0.4
HE1 A:HIS54 4.1 50.0 1.0
OE1 A:GLU144 4.3 31.5 1.0
HG3 A:GLU58 4.3 22.9 0.1
O A:HOH493 4.3 46.6 1.0
O A:HOH305 4.3 53.4 1.0
CG A:HIS54 4.5 25.8 1.0
CD A:GLN55 4.6 22.2 1.0
HE1 A:PHE51 4.6 18.8 1.0
OE2 A:GLU144 4.6 43.2 1.0
ND1 A:HIS54 4.7 39.8 1.0
OE1 A:GLN55 4.9 38.3 1.0
CD A:GLU144 4.9 29.7 1.0
CD A:GLU58 5.0 40.1 0.4

Reference:

E.De Meulenaere, J.B.Bailey, F.A.Tezcan, D.D.Deheyn. First Biochemical and Crystallographic Characterization of A Fast-Performing Ferritin From A Marine Invertebrate. Biochem. J. V. 474 4193 2017.
ISSN: ESSN 1470-8728
PubMed: 29127253
DOI: 10.1042/BCJ20170681
Page generated: Mon Oct 28 14:36:55 2024

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