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Zinc in PDB 1u0l: Crystal Structure of Yjeq From Thermotoga Maritima

Protein crystallography data

The structure of Crystal Structure of Yjeq From Thermotoga Maritima, PDB code: 1u0l was solved by D.H.Shin, Y.Lou, J.Jaru, R.Kim, H.Yokota, S.H.Kim, Berkeleystructural Genomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.819, 114.798, 77.088, 90.00, 105.72, 90.00
R / Rfree (%) 21.8 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Yjeq From Thermotoga Maritima (pdb code 1u0l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Yjeq From Thermotoga Maritima, PDB code: 1u0l:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1u0l

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Zinc binding site 1 out of 3 in the Crystal Structure of Yjeq From Thermotoga Maritima


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 Yjeq From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn298

b:62.4
occ:1.00
SG A:CYS250 2.3 38.0 1.0
SG A:CYS255 2.3 63.5 1.0
SG A:CYS263 2.4 54.1 1.0
ND1 A:HIS257 2.4 65.6 1.0
CB A:CYS263 3.1 57.6 1.0
CB A:CYS255 3.1 62.0 1.0
CE1 A:HIS257 3.2 67.1 1.0
CB A:CYS250 3.2 50.0 1.0
CG A:HIS257 3.3 65.5 1.0
CA A:HIS257 3.3 42.5 1.0
N A:HIS257 3.4 41.1 1.0
CB A:HIS257 3.6 63.6 1.0
CA A:CYS263 3.7 59.1 1.0
O A:CYS255 3.7 56.3 1.0
C A:CYS255 4.0 55.4 1.0
CA A:CYS255 4.2 57.1 1.0
NE2 A:HIS257 4.2 67.5 1.0
CD2 A:HIS257 4.3 66.1 1.0
C A:CYS263 4.4 57.7 1.0
N A:GLY264 4.5 76.3 1.0
O A:GLU262 4.6 70.7 1.0
CB A:VAL265 4.6 32.3 1.0
C A:ASN256 4.6 37.5 1.0
CA A:CYS250 4.6 63.6 1.0
C A:HIS257 4.6 42.6 1.0
N A:ASN256 4.7 40.0 1.0
N A:VAL265 4.7 39.8 1.0
CG2 A:VAL265 4.8 31.0 1.0
N A:CYS263 4.9 61.0 1.0

Zinc binding site 2 out of 3 in 1u0l

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Zinc binding site 2 out of 3 in the Crystal Structure of Yjeq From Thermotoga Maritima


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 Yjeq From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn598

b:41.5
occ:1.00
SG B:CYS563 2.2 31.9 1.0
ND1 B:HIS557 2.2 29.8 1.0
SG B:CYS550 2.5 81.1 1.0
SG B:CYS555 2.5 38.5 1.0
CE1 B:HIS557 2.9 29.2 1.0
CB B:CYS555 3.0 44.2 1.0
CB B:CYS550 3.2 77.7 1.0
CG B:HIS557 3.4 30.7 1.0
CB B:CYS563 3.4 41.7 1.0
CA B:HIS557 3.7 35.1 1.0
N B:HIS557 3.9 37.0 1.0
CB B:HIS557 3.9 31.8 1.0
CA B:CYS563 4.0 50.8 1.0
N B:GLY564 4.1 47.9 1.0
NE2 B:HIS557 4.2 30.1 1.0
O B:CYS555 4.2 50.5 1.0
C B:CYS555 4.2 51.8 1.0
CA B:CYS555 4.2 53.7 1.0
CG2 B:VAL565 4.3 47.2 1.0
CD2 B:HIS557 4.4 30.8 1.0
N B:VAL565 4.4 45.3 1.0
CB B:VAL565 4.5 47.3 1.0
CA B:CYS550 4.5 63.5 1.0
C B:CYS563 4.5 50.2 1.0
O B:GLU562 4.8 83.6 1.0
N B:ASN556 4.9 50.4 1.0
C B:ASN556 4.9 45.7 1.0

Zinc binding site 3 out of 3 in 1u0l

Go back to Zinc Binding Sites List in 1u0l
Zinc binding site 3 out of 3 in the Crystal Structure of Yjeq From Thermotoga Maritima


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 Yjeq From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn898

b:51.5
occ:1.00
ND1 C:HIS857 2.3 34.3 1.0
SG C:CYS863 2.3 49.6 1.0
SG C:CYS855 2.3 60.3 1.0
SG C:CYS850 2.4 59.3 1.0
CB C:CYS850 2.9 60.6 1.0
CE1 C:HIS857 2.9 36.5 1.0
CB C:CYS855 3.1 62.8 1.0
CB C:CYS863 3.3 53.9 1.0
CG C:HIS857 3.5 37.0 1.0
CA C:CYS863 3.5 68.6 1.0
CA C:HIS857 3.8 46.6 1.0
N C:HIS857 3.8 46.9 1.0
CB C:HIS857 4.0 39.5 1.0
N C:GLY864 4.2 0.9 1.0
NE2 C:HIS857 4.2 36.6 1.0
O C:CYS855 4.2 49.6 1.0
C C:CYS863 4.3 69.4 1.0
C C:CYS855 4.3 50.5 1.0
CA C:CYS855 4.3 52.0 1.0
CA C:CYS850 4.3 66.5 1.0
CD2 C:HIS857 4.4 37.5 1.0
N C:VAL865 4.6 61.0 1.0
CB C:VAL865 4.7 51.6 1.0
N C:CYS863 4.7 70.2 1.0
CG2 C:VAL865 4.7 52.0 1.0
N C:ASN856 4.9 41.1 1.0
C C:ASN856 4.9 38.2 1.0
CB C:GLU860 5.0 71.4 1.0

Reference:

D.H.Shin, Y.Lou, J.Jancarik, H.Yokota, R.Kim, S.H.Kim. Crystal Structure of Yjeq From Thermotoga Maritima Contains A Circularly Permuted Gtpase Domain Proc.Natl.Acad.Sci.Usa V. 101 13198 2004.
ISSN: ISSN 0027-8424
PubMed: 15331784
DOI: 10.1073/PNAS.0405202101
Page generated: Wed Dec 16 03:06:10 2020

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