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Zinc in PDB 1x1c: Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+

Protein crystallography data

The structure of Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+, PDB code: 1x1c was solved by H.Yamaguchi, K.Wada, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.83 / 2.85
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.615, 81.615, 250.960, 90.00, 90.00, 120.00
R / Rfree (%) 23 / 28.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+ (pdb code 1x1c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+, PDB code: 1x1c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1x1c

Go back to Zinc Binding Sites List in 1x1c
Zinc binding site 1 out of 5 in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+


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 Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5001

b:70.1
occ:0.36
NE2 A:HIS150 2.9 56.0 1.0
CE1 A:HIS290 3.6 72.5 1.0
CD2 A:HIS150 3.8 58.1 1.0
CE1 A:HIS150 3.9 62.1 1.0
ND1 A:HIS290 4.3 63.2 1.0
CD1 A:PHE146 4.4 70.3 1.0
NE2 A:HIS290 4.4 64.7 1.0
CE1 A:PHE146 4.7 65.8 1.0
ZN A:ZN5004 4.8 65.2 0.1

Zinc binding site 2 out of 5 in 1x1c

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Zinc binding site 2 out of 5 in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+


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 Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5002

b:73.5
occ:0.32
NE2 A:HIS290 2.1 64.7 1.0
OD1 A:ASP286 2.3 61.3 1.0
CD2 A:HIS290 2.9 65.1 1.0
CG A:ASP286 3.0 65.4 1.0
OD2 A:ASP286 3.1 54.4 1.0
CE1 A:HIS290 3.1 72.5 1.0
O A:ASP286 3.9 67.0 1.0
CG A:HIS290 4.1 50.9 1.0
ND1 A:HIS290 4.2 63.2 1.0
CB A:ASP286 4.4 55.7 1.0
C A:ASP286 4.5 61.4 1.0
CA A:ASP286 4.8 59.2 1.0

Zinc binding site 3 out of 5 in 1x1c

Go back to Zinc Binding Sites List in 1x1c
Zinc binding site 3 out of 5 in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+


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 Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5003

b:54.0
occ:0.23
NE2 A:HIS190 2.4 72.2 1.0
CD2 A:HIS190 3.2 60.3 1.0
CE1 A:HIS190 3.5 70.7 1.0
CG A:HIS190 4.4 63.3 1.0
ND1 A:HIS190 4.5 65.5 1.0
O A:ALA186 4.6 65.5 1.0
CD1 A:LEU162 4.8 54.9 1.0
CB A:LYS189 4.8 54.2 1.0

Zinc binding site 4 out of 5 in 1x1c

Go back to Zinc Binding Sites List in 1x1c
Zinc binding site 4 out of 5 in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+


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 Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5004

b:65.2
occ:0.15
ND1 A:HIS290 4.6 63.2 1.0
CZ A:TYR135 4.6 0.8 1.0
CE2 A:TYR135 4.7 0.3 1.0
CD1 A:LEU302 4.8 49.7 1.0
OH A:TYR135 4.8 0.7 1.0
ZN A:ZN5001 4.8 70.1 0.4
CE1 A:TYR135 4.9 0.8 1.0

Zinc binding site 5 out of 5 in 1x1c

Go back to Zinc Binding Sites List in 1x1c
Zinc binding site 5 out of 5 in the Crystal Structure of Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+


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 Bchu Complexed with S-Adenosyl-L-Homocysteine and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5005

b:41.1
occ:0.17
CE1 A:HIS11 2.1 60.3 1.0
NE2 A:HIS11 2.4 48.4 1.0
ND1 A:HIS11 3.3 69.5 1.0
CD2 A:HIS11 3.7 71.1 1.0
CG A:HIS11 4.2 63.9 1.0

Reference:

K.Wada, H.Yamaguchi, J.Harada, K.Niimi, S.Osumi, Y.Saga, H.Oh-Oka, H.Tamiaki, K.Fukuyama. Crystal Structures of Bchu, A Methyltransferase Involved in Bacteriochlorophyll C Biosynthesis, and Its Complex with S-Adenosylhomocysteine: Implications For Reaction Mechanism. J.Mol.Biol. V. 360 839 2006.
ISSN: ISSN 0022-2836
PubMed: 16797589
DOI: 10.1016/J.JMB.2006.05.057
Page generated: Wed Dec 16 03:10:54 2020

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