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Zinc in PDB 5cmq: Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star

Enzymatic activity of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star

All present enzymatic activity of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star, PDB code: 5cmq was solved by P.A.Sontz, J.B.Bailey, S.Ahn, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.04 / 1.94
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.210, 180.210, 180.210, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 18

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star (pdb code 5cmq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star, PDB code: 5cmq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5cmq

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Zinc binding site 1 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:14.5
occ:1.00
 O A:HOH371 1.9 15.8 1.0
OE2 A:GLU62 2.0 13.3 1.0
OE1 A:GLU27 2.0 12.2 1.0
O A:HOH306 2.1 12.5 1.0
ND1 A:HIS65 2.1 13.6 1.0
CD A:GLU27 3.0 12.1 1.0
CD A:GLU62 3.0 13.7 1.0
CE1 A:HIS65 3.1 15.0 1.0
CG A:HIS65 3.2 13.2 1.0
OE2 A:GLU27 3.3 13.0 1.0
ZN A:ZN208 3.3 29.1 0.5
OE1 A:GLU62 3.4 16.8 1.0
CB A:HIS65 3.5 12.7 1.0
OE1 A:GLN141 4.0 23.8 1.0
O A:HOH416 4.1 21.6 1.0
CG1 A:VAL110 4.2 13.9 1.0
NE2 A:HIS65 4.2 13.7 1.0
CD2 A:HIS65 4.3 13.0 1.0
CG A:GLU27 4.3 11.1 1.0
CG A:GLU62 4.4 12.4 1.0
CA A:GLU62 4.5 11.5 1.0
O A:HOH430 4.5 14.8 1.0
CB A:GLU62 4.7 11.7 1.0
CB A:GLU27 4.7 10.9 1.0
CD A:GLN141 4.9 20.9 1.0
CA A:GLU27 4.9 10.7 1.0

Zinc binding site 2 out of 9 in 5cmq

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Zinc binding site 2 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:50.3
occ:0.50
 NE2 A:HIS105 2.2 35.9 1.0
O A:HOH444 2.7 49.2 1.0
CD2 A:HIS105 3.1 27.7 1.0
CE1 A:HIS105 3.3 33.2 1.0
CG A:HIS105 4.3 27.1 1.0
ND1 A:HIS105 4.4 31.3 1.0
O A:HOH398 4.4 31.2 1.0
O A:HOH524 4.7 27.7 1.0

Zinc binding site 3 out of 9 in 5cmq

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Zinc binding site 3 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:37.1
occ:0.33
 NE2 A:HIS122 2.2 31.7 1.0
CE1 A:HIS122 2.8 35.3 1.0
O A:HOH520 2.8 43.4 0.3
CD2 A:HIS122 3.5 31.6 1.0
ND1 A:HIS122 4.0 36.4 1.0
CG A:HIS122 4.4 30.3 1.0
O A:HOH404 4.9 46.2 1.0

Zinc binding site 4 out of 9 in 5cmq

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Zinc binding site 4 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:47.2
occ:0.33
 OE2 A:GLU134 2.3 23.5 1.0
OD1 A:ASP131 2.7 29.4 1.0
O A:HOH308 3.1 40.9 1.0
CD A:GLU134 3.6 19.9 1.0
CG A:ASP131 3.8 28.6 1.0
OE1 A:GLU134 4.2 24.3 1.0
CB A:ASP131 4.5 20.7 1.0
CB A:GLU134 4.6 18.7 1.0
CG A:GLU134 4.7 20.0 1.0
OD2 A:ASP131 4.7 21.9 1.0
CA A:ASP131 4.8 17.5 1.0
O A:HOH329 5.0 35.8 1.0

Zinc binding site 5 out of 9 in 5cmq

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Zinc binding site 5 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:31.1
occ:0.20
 ZN A:ZN206 2.3 30.0 0.2
NE2 A:HIS173 2.5 26.1 1.0
CE1 A:HIS173 2.7 28.0 1.0
CD2 A:HIS173 3.9 23.7 1.0
ND1 A:HIS173 4.0 25.2 1.0
CG A:HIS173 4.6 22.2 1.0

Zinc binding site 6 out of 9 in 5cmq

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Zinc binding site 6 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:30.0
occ:0.20
 ZN A:ZN205 2.3 31.1 0.2
NE2 A:HIS173 3.4 26.1 1.0
CD2 A:LEU169 3.9 11.8 1.0
CE1 A:HIS173 4.2 28.0 1.0
CD2 A:HIS173 4.3 23.7 1.0
CD1 A:LEU169 4.7 11.4 1.0
CG A:LEU169 4.9 11.0 1.0

Zinc binding site 7 out of 9 in 5cmq

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Zinc binding site 7 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:46.9
occ:0.50
 OD2 A:ASP84 2.3 19.9 1.0
OD1 A:ASP84 2.7 14.2 1.0
CG A:ASP84 2.8 15.4 1.0
O A:HOH319 4.2 29.9 0.5
CB A:ASP84 4.2 13.7 1.0
O A:HOH344 4.4 20.2 1.0

Zinc binding site 8 out of 9 in 5cmq

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Zinc binding site 8 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:29.1
occ:0.50
 O A:HOH371 1.9 15.8 1.0
OE1 A:GLU62 1.9 16.8 1.0
OE2 A:GLU107 2.2 22.6 1.0
ZN A:ZN209 2.3 25.0 0.5
O A:HOH430 2.5 14.8 1.0
OE1 A:GLU107 2.5 18.5 1.0
CD A:GLU107 2.7 18.2 1.0
CD A:GLU62 2.9 13.7 1.0
OE2 A:GLU62 3.2 13.3 1.0
ZN A:ZN201 3.3 14.5 1.0
OE1 A:GLN141 3.5 23.8 1.0
CE1 A:HIS65 4.1 15.0 1.0
NE2 A:GLN141 4.1 19.7 1.0
CG A:GLU62 4.2 12.4 1.0
CG A:GLU107 4.2 14.8 1.0
CD A:GLN141 4.2 20.9 1.0
ND1 A:HIS65 4.3 13.6 1.0
O A:HOH306 4.5 12.5 1.0
O A:HOH440 4.5 24.2 1.0
OE1 A:GLN58 4.6 39.5 1.0
CE2 A:TYR34 4.6 13.1 1.0
OH A:TYR34 4.8 17.8 1.0
CB A:GLU107 4.9 14.8 1.0

Zinc binding site 9 out of 9 in 5cmq

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Zinc binding site 9 out of 9 in the Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Zn-Bound Human H-Ferritin Variant 122H-Delta C- Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:25.0
occ:0.50
 O A:HOH430 2.2 14.8 1.0
ZN A:ZN208 2.3 29.1 0.5
OE1 A:GLN58 2.5 39.5 1.0
O A:HOH440 2.5 24.2 1.0
OE1 A:GLU62 2.5 16.8 1.0
OE1 A:GLU107 2.5 18.5 1.0
CD A:GLU107 3.4 18.2 1.0
OE2 A:GLU107 3.6 22.6 1.0
CD A:GLN58 3.6 34.9 1.0
CD A:GLU62 3.7 13.7 1.0
O A:HOH371 4.1 15.8 1.0
OH A:TYR34 4.2 17.8 1.0
NE2 A:GLN58 4.2 32.5 1.0
O A:HOH467 4.2 39.8 1.0
CE2 A:TYR34 4.2 13.1 1.0
OE2 A:GLU140 4.2 38.0 1.0
CE1 A:HIS65 4.3 15.0 1.0
CB A:ALA144 4.4 13.7 1.0
CG A:GLU62 4.4 12.4 1.0
OE2 A:GLU62 4.5 13.3 1.0
OE1 A:GLU61 4.5 42.3 1.0
CZ A:TYR34 4.6 15.8 1.0
CG A:GLU107 4.7 14.8 1.0
CG A:GLN58 4.9 22.7 1.0
OE1 A:GLN141 4.9 23.8 1.0
O A:HOH436 5.0 20.3 1.0

Reference:

P.A.Sontz, J.B.Bailey, S.Ahn, F.A.Tezcan. A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals. J.Am.Chem.Soc. V. 137 11598 2015.
ISSN: ESSN 1520-5126
PubMed: 26305584
DOI: 10.1021/JACS.5B07463
Page generated: Sun Oct 27 14:23:57 2024

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