Atomistry » Zinc » PDB 2ytt-2z3j » 2yx1
Atomistry »
  Zinc »
    PDB 2ytt-2z3j »
      2yx1 »

Zinc in PDB 2yx1: Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase

Protein crystallography data

The structure of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase, PDB code: 2yx1 was solved by S.Goto-Ito, T.Ito, R.Ishii, Y.Bessho, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.000, 69.790, 87.150, 90.00, 96.07, 90.00
R / Rfree (%) 22.4 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase (pdb code 2yx1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase, PDB code: 2yx1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 1 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:33.8
occ:1.00
OE1 A:GLU230 2.0 32.9 1.0
ND1 A:HIS227 2.1 14.2 1.0
O A:HOH632 2.3 38.6 1.0
CE1 A:HIS227 3.0 31.4 1.0
CG A:HIS227 3.1 28.9 1.0
CD A:GLU230 3.1 52.5 1.0
CB A:HIS227 3.5 30.2 1.0
OE2 A:GLU230 3.6 39.2 1.0
CA A:HIS227 3.7 28.1 1.0
NE2 A:HIS227 4.1 21.6 1.0
CD2 A:HIS227 4.2 25.6 1.0
CG A:GLU230 4.4 41.0 1.0
N A:HIS227 4.5 26.2 1.0
O A:HOH579 4.6 44.6 1.0
CB A:GLU230 4.7 35.6 1.0
C A:HIS227 4.9 33.8 1.0

Zinc binding site 2 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 2 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:31.5
occ:1.00
ND1 A:HIS243 2.1 31.5 1.0
O A:HOH505 2.5 21.5 1.0
O A:HOH625 2.5 21.9 1.0
CE1 A:HIS243 3.0 41.5 1.0
CG A:HIS243 3.1 35.2 1.0
CB A:HIS243 3.4 32.0 1.0
CA A:HIS243 3.7 25.2 1.0
O A:HOH630 4.0 48.8 1.0
O A:GLU242 4.1 21.2 1.0
NE2 A:HIS243 4.1 42.7 1.0
CD2 A:HIS243 4.2 31.8 1.0
N A:HIS243 4.5 21.8 1.0
C A:GLU242 4.7 25.0 1.0
C A:HIS243 4.8 29.7 1.0
O A:HIS243 5.0 30.9 1.0

Zinc binding site 3 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 3 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:77.3
occ:1.00
O A:PHE303 2.2 44.7 1.0
SG A:CYS307 2.4 42.7 1.0
SG A:CYS309 2.5 42.9 1.0
O A:CYS307 2.6 30.8 1.0
C A:PHE303 2.9 36.7 1.0
C A:CYS307 3.0 26.5 1.0
CB A:CYS309 3.2 39.8 1.0
N A:CYS307 3.4 28.8 1.0
CA A:CYS307 3.5 27.2 1.0
CB A:CYS307 3.5 38.9 1.0
N A:CYS309 3.7 44.9 1.0
N A:GLU304 3.7 41.9 1.0
CA A:PHE303 3.7 36.8 1.0
CB A:PHE303 3.7 38.3 1.0
CA A:GLU304 3.9 47.4 1.0
N A:ASP308 3.9 32.9 1.0
C A:ASP308 4.0 44.8 1.0
CA A:CYS309 4.0 39.0 1.0
CA A:ASP308 4.3 42.2 1.0
C A:GLU304 4.3 45.3 1.0
CD2 A:PHE303 4.4 30.4 1.0
C A:LYS306 4.4 37.4 1.0
O A:GLU304 4.5 48.3 1.0
O A:HOH616 4.5 41.9 1.0
CG A:PHE303 4.6 33.1 1.0
O A:ASP308 4.6 41.8 1.0
N A:LYS306 4.8 45.9 1.0
CA A:LYS306 5.0 39.8 1.0

Zinc binding site 4 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 4 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:53.4
occ:1.00
NE A:SFG401 2.2 22.4 1.0
CD A:SFG401 3.0 26.0 1.0
CD2 A:TYR177 3.1 71.4 1.0
CE2 A:TYR177 3.2 73.9 1.0
C5' A:SFG401 3.3 26.4 1.0
O A:HOH570 4.2 26.0 1.0
CD A:PRO267 4.2 30.6 1.0
O A:HOH626 4.3 41.4 1.0
CG A:TYR177 4.3 63.2 1.0
O A:ASN265 4.4 18.4 1.0
CG A:SFG401 4.4 19.9 1.0
CZ A:TYR177 4.4 71.1 1.0
O A:HOH596 4.7 36.1 1.0
C4' A:SFG401 4.7 23.6 1.0
CD1 A:LEU266 4.7 21.1 1.0
CA A:LEU266 4.7 30.1 1.0
CB A:SFG401 4.9 20.8 1.0
O A:HOH544 4.9 29.1 1.0
CB A:TYR177 5.0 51.8 1.0

Zinc binding site 5 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 5 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:39.1
occ:1.00
ND1 B:HIS11 2.0 40.2 1.0
CE1 B:HIS11 2.9 26.5 1.0
CG B:HIS11 3.0 34.0 1.0
CB B:HIS11 3.3 35.3 1.0
CA B:HIS11 3.8 28.1 1.0
CG2 B:ILE56 4.0 45.8 1.0
O B:HOH550 4.0 34.1 1.0
NE2 B:HIS11 4.0 49.2 1.0
CD2 B:HIS11 4.1 34.0 1.0
CB B:GLN14 4.4 27.9 1.0
CG B:GLN14 4.4 25.9 1.0
O B:HOH514 4.5 23.0 1.0
O B:LYS10 4.7 37.0 1.0
N B:HIS11 4.8 37.8 1.0
O B:HIS11 4.8 37.0 1.0
C B:HIS11 4.8 38.5 1.0

Zinc binding site 6 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 6 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:47.9
occ:1.00
OE1 B:GLU230 2.1 47.4 1.0
ND1 B:HIS227 2.5 44.6 1.0
CD B:GLU230 2.9 49.6 1.0
OE2 B:GLU230 3.1 57.7 1.0
CE1 B:HIS227 3.3 46.9 1.0
CG B:HIS227 3.3 36.8 1.0
NZ B:LYS175 3.4 66.7 1.0
CB B:HIS227 3.6 36.0 1.0
CA B:HIS227 3.7 32.5 1.0
CG B:GLU230 4.2 39.6 1.0
O B:HOH544 4.2 53.7 1.0
CE B:LYS175 4.3 60.8 1.0
NE2 B:HIS227 4.3 55.0 1.0
CD2 B:HIS227 4.3 48.7 1.0
CB B:GLU230 4.5 42.5 1.0
N B:HIS227 4.5 33.1 1.0
C B:HIS227 4.9 41.1 1.0
O B:HIS227 5.0 34.0 1.0

Zinc binding site 7 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 7 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn507

b:70.3
occ:1.00
O B:PHE303 2.1 52.2 1.0
SG B:CYS309 2.4 47.9 1.0
SG B:CYS307 2.6 50.1 1.0
O B:CYS307 2.7 51.6 1.0
C B:PHE303 2.8 50.5 1.0
C B:CYS307 3.1 44.6 1.0
CB B:CYS309 3.1 23.0 1.0
N B:CYS307 3.4 43.6 1.0
CA B:CYS307 3.5 41.2 1.0
N B:GLU304 3.5 49.6 1.0
N B:CYS309 3.6 37.4 1.0
CB B:CYS307 3.6 44.6 1.0
CA B:GLU304 3.7 45.7 1.0
CB B:PHE303 3.7 45.3 1.0
CA B:PHE303 3.7 45.3 1.0
N B:ASP308 3.9 36.1 1.0
CA B:CYS309 3.9 35.3 1.0
C B:ASP308 4.2 43.8 1.0
C B:GLU304 4.2 47.1 1.0
O B:GLU304 4.3 43.4 1.0
CD2 B:PHE303 4.4 43.7 1.0
C B:LYS306 4.5 52.0 1.0
CA B:ASP308 4.5 46.1 1.0
CG B:PHE303 4.6 45.9 1.0
N B:LYS306 4.8 55.2 1.0
O B:ASP308 5.0 46.3 1.0

Zinc binding site 8 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 8 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:67.5
occ:1.00
NE B:SFG402 2.4 35.8 1.0
CD B:SFG402 3.3 21.1 1.0
C5' B:SFG402 3.6 20.2 1.0
O B:HOH554 3.8 34.6 1.0
O B:HOH540 3.8 37.0 1.0
CD B:PRO267 4.3 32.9 1.0
CD2 B:TYR177 4.4 64.8 1.0
O B:ASN265 4.5 31.8 1.0
O B:HOH590 4.6 53.5 1.0
CG B:TYR177 4.6 63.6 1.0
CG B:SFG402 4.7 29.8 1.0
CB B:TYR177 4.7 46.0 1.0
CE2 B:TYR177 4.8 66.2 1.0
CG B:PRO267 4.8 42.1 1.0
CD1 B:LEU266 4.9 33.4 1.0
O B:HOH576 4.9 46.8 1.0
CA B:LEU266 4.9 33.4 1.0
C4' B:SFG402 5.0 25.9 1.0

Zinc binding site 9 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 9 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


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 M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn509

b:80.2
occ:1.00
NE2 B:HIS271 2.5 48.9 1.0
NZ B:LYS272 2.7 68.6 1.0
O B:HOH560 3.3 54.1 1.0
CE1 B:HIS271 3.3 39.7 1.0
CD2 B:HIS271 3.5 42.3 1.0
CE B:LYS272 3.6 66.6 1.0
CG B:LYS272 4.2 55.0 1.0
CD B:LYS272 4.4 55.7 1.0
ND1 B:HIS271 4.5 37.1 1.0
CG B:HIS271 4.6 39.4 1.0

Zinc binding site 10 out of 10 in 2yx1

Go back to Zinc Binding Sites List in 2yx1
Zinc binding site 10 out of 10 in the Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of M.Jannaschii Trna M1G37 Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn510

b:71.6
occ:1.00
NZ B:LYS318 2.5 55.3 1.0
CE B:LYS318 3.1 48.9 1.0
O B:HOH590 4.0 53.5 1.0
CD1 B:LEU182 4.1 36.7 1.0
O B:HOH551 4.1 40.3 1.0
CB B:SER179 4.4 39.0 1.0
OG B:SER179 4.5 42.0 1.0
CD2 B:LEU182 4.6 35.4 1.0
CD B:LYS318 4.6 49.6 1.0
CG B:PRO267 4.7 42.1 1.0
O B:HOH554 4.7 34.6 1.0
CG1 B:ILE326 4.9 44.6 1.0
CG B:LEU182 5.0 35.2 1.0

Reference:

S.Goto-Ito, T.Ito, R.Ishii, Y.Muto, Y.Bessho, S.Yokoyama. Crystal Structure of Archaeal Trna(M(1)G37)Methyltransferase ATRM5. Proteins V. 72 1274 2008.
ISSN: ISSN 0887-3585
PubMed: 18384044
DOI: 10.1002/PROT.22019
Page generated: Wed Dec 16 04:03:45 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy