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Zinc in PDB 4u8u: The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.

Protein crystallography data

The structure of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution., PDB code: 4u8u was solved by J.F.R.Bachega, F.V.Maluf, B.Andi, H.D'muniz Pereira, M.F.Carazzollea, A.Orville, M.Tabak, R.C.Garratt, E.Horjales, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.66 / 3.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 272.680, 319.900, 333.180, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.5

Other elements in 4u8u:

The structure of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. also contains other interesting chemical elements:

Iron (Fe) 36 atoms
Calcium (Ca) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. (pdb code 4u8u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution., PDB code: 4u8u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4u8u

Go back to Zinc Binding Sites List in 4u8u
Zinc binding site 1 out of 6 in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn302

b:28.0
occ:1.00
NE2 O:HIS94 2.1 51.9 1.0
OD1 O:ASP90 2.1 35.0 1.0
NE2 O:HIS64 2.2 20.4 1.0
O O:HOH401 2.2 28.0 1.0
CE1 O:HIS64 2.7 20.4 1.0
CE1 O:HIS94 2.9 51.9 1.0
CG O:ASP90 3.1 35.0 1.0
CD2 O:HIS94 3.2 51.9 1.0
CD2 O:HIS64 3.4 20.4 1.0
O O:GLN65 3.5 28.0 1.0
OD2 O:ASP90 3.5 35.0 1.0
ND1 O:HIS64 3.9 20.4 1.0
ND1 O:HIS94 4.1 51.9 1.0
CG O:HIS94 4.2 51.9 1.0
CG O:HIS64 4.3 20.4 1.0
CB O:ASP90 4.4 35.0 1.0
C O:GLN65 4.5 28.0 1.0
O O:ASP90 4.6 19.8 1.0
CA O:CYS66 4.7 15.2 1.0
O O:CYS66 4.7 15.2 1.0
C O:CYS66 4.8 15.2 1.0
C O:ASP90 5.0 19.8 1.0

Zinc binding site 2 out of 6 in 4u8u

Go back to Zinc Binding Sites List in 4u8u
Zinc binding site 2 out of 6 in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn303

b:28.0
occ:1.00
NE2 O:HIS144 2.1 13.6 1.0
NE2 O:HIS142 2.1 20.5 1.0
CE1 O:HIS142 3.0 20.5 1.0
CE1 O:HIS144 3.0 13.6 1.0
CD2 O:HIS144 3.1 13.6 1.0
CD2 O:HIS142 3.2 20.5 1.0
CB O:PRO161 3.8 28.0 1.0
ND1 O:HIS142 4.1 20.5 1.0
ND1 O:HIS144 4.1 13.6 1.0
CG O:HIS144 4.2 13.6 1.0
CG O:HIS142 4.3 20.5 1.0
CA O:PRO161 4.7 28.0 1.0
CG O:PRO161 4.8 28.0 1.0
CG O:GLU127 4.9 35.6 1.0

Zinc binding site 3 out of 6 in 4u8u

Go back to Zinc Binding Sites List in 4u8u
Zinc binding site 3 out of 6 in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Zn302

b:28.0
occ:1.00
NE2 s:HIS144 2.0 28.0 1.0
NE2 c:HIS236 2.1 49.5 1.0
NE2 s:HIS142 2.1 28.0 1.0
O c:HOH401 2.1 28.0 1.0
CD2 c:HIS236 2.7 49.5 1.0
CE1 s:HIS142 3.0 28.0 1.0
CE1 s:HIS144 3.0 28.0 1.0
CD2 s:HIS144 3.1 28.0 1.0
CD2 s:HIS142 3.2 28.0 1.0
CE1 c:HIS236 3.3 49.5 1.0
CB s:PRO161 3.8 28.0 1.0
CG c:HIS236 4.0 49.5 1.0
ND1 s:HIS144 4.1 28.0 1.0
ND1 s:HIS142 4.1 28.0 1.0
CG s:HIS144 4.2 28.0 1.0
ND1 c:HIS236 4.2 49.5 1.0
CG s:HIS142 4.3 28.0 1.0
CD1 c:ILE117 4.4 28.0 1.0
CA s:PRO161 4.7 16.1 1.0
CG s:PRO161 4.8 28.0 1.0
CG s:GLU127 4.8 30.5 1.0

Zinc binding site 4 out of 6 in 4u8u

Go back to Zinc Binding Sites List in 4u8u
Zinc binding site 4 out of 6 in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn302

b:28.0
occ:1.00
NE2 d:HIS94 2.1 62.7 1.0
OD1 d:ASP90 2.1 20.9 1.0
NE2 d:HIS64 2.2 28.0 1.0
O d:HOH401 2.2 28.0 1.0
CE1 d:HIS64 2.7 28.0 1.0
CE1 d:HIS94 2.9 62.7 1.0
CG d:ASP90 3.1 20.9 1.0
CD2 d:HIS94 3.2 62.7 1.0
CD2 d:HIS64 3.4 28.0 1.0
O d:GLN65 3.5 28.0 1.0
OD2 d:ASP90 3.5 20.9 1.0
ND1 d:HIS64 3.9 28.0 1.0
ND1 d:HIS94 4.1 62.7 1.0
CG d:HIS94 4.2 62.7 1.0
CG d:HIS64 4.3 28.0 1.0
CB d:ASP90 4.4 20.9 1.0
C d:GLN65 4.5 28.0 1.0
O d:ASP90 4.6 26.1 1.0
CA d:CYS66 4.7 18.5 1.0
O d:CYS66 4.7 18.5 1.0
C d:CYS66 4.8 18.5 1.0
C d:ASP90 4.9 26.1 1.0
N d:CYS66 5.0 18.5 1.0

Zinc binding site 5 out of 6 in 4u8u

Go back to Zinc Binding Sites List in 4u8u
Zinc binding site 5 out of 6 in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn303

b:28.0
occ:1.00
NE2 d:HIS144 2.1 28.0 1.0
NE2 d:HIS142 2.1 28.0 1.0
O d:HOH402 2.1 28.0 1.0
CE1 d:HIS142 3.0 28.0 1.0
CE1 d:HIS144 3.0 28.0 1.0
CD2 d:HIS144 3.1 28.0 1.0
CD2 d:HIS142 3.2 28.0 1.0
CB d:PRO161 3.8 28.0 1.0
ND1 d:HIS142 4.1 28.0 1.0
ND1 d:HIS144 4.2 28.0 1.0
CG d:HIS144 4.2 28.0 1.0
CG d:HIS142 4.3 28.0 1.0
CA d:PRO161 4.7 20.9 1.0
CG d:PRO161 4.8 28.0 1.0
CG d:GLU127 4.9 19.3 1.0

Zinc binding site 6 out of 6 in 4u8u

Go back to Zinc Binding Sites List in 4u8u
Zinc binding site 6 out of 6 in the The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystallographic Structure of the Giant Hemoglobin From Glossoscolex Paulistus at 3.2 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
s:Zn302

b:28.0
occ:1.00
NE2 s:HIS94 2.1 58.1 1.0
OD1 s:ASP90 2.1 17.3 1.0
O s:HOH401 2.2 28.0 1.0
NE2 s:HIS64 2.2 14.3 1.0
CE1 s:HIS64 2.8 14.3 1.0
CE1 s:HIS94 2.9 58.1 1.0
CG s:ASP90 3.1 17.3 1.0
CD2 s:HIS94 3.2 58.1 1.0
CD2 s:HIS64 3.5 14.3 1.0
O s:GLN65 3.5 28.0 1.0
OD2 s:ASP90 3.5 17.3 1.0
ND1 s:HIS64 4.0 14.3 1.0
ND1 s:HIS94 4.1 58.1 1.0
CG s:HIS94 4.3 58.1 1.0
CG s:HIS64 4.3 14.3 1.0
CB s:ASP90 4.4 17.3 1.0
C s:GLN65 4.5 28.0 1.0
O s:CYS66 4.7 20.1 1.0
O s:ASP90 4.7 20.4 1.0
CA s:CYS66 4.7 20.1 1.0
C s:CYS66 4.8 20.1 1.0
C s:ASP90 5.0 20.4 1.0

Reference:

J.F.Ruggiero Bachega, F.Vasconcelos Maluf, B.Andi, H.D'muniz Pereira, M.Falsarella Carazzollea, A.M.Orville, M.Tabak, J.Brandao-Neto, R.C.Garratt, E.Horjales Reboredo. The Structure of the Giant Haemoglobin From Glossoscolex Paulistus. Acta Crystallogr.,Sect.D V. 71 1257 2015.
ISSN: ESSN 1399-0047
PubMed: 26057666
DOI: 10.1107/S1399004715005453
Page generated: Wed Dec 16 05:48:01 2020

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