Atomistry » Manganese » PDB 1ss9-1uvi » 1stx
Atomistry »
  Manganese »
    PDB 1ss9-1uvi »
      1stx »

Manganese in PDB 1stx: Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+

Enzymatic activity of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+

All present enzymatic activity of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+:
3.1.21.4;

Protein crystallography data

The structure of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+, PDB code: 1stx was solved by N.C.Horton, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.710, 58.690, 82.100, 90.00, 107.70, 90.00
R / Rfree (%) 20.1 / 26.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ (pdb code 1stx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+, PDB code: 1stx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1stx

Go back to Manganese Binding Sites List in 1stx
Manganese binding site 1 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1003

b:38.1
occ:1.00
 OP1 D:DA7 1.9 56.6 1.0
OE2 A:GLU45 2.0 34.5 1.0
OD2 A:ASP74 2.3 22.4 1.0
O A:ILE91 2.5 24.5 1.0
P D:DA7 2.8 54.1 1.0
CD A:GLU45 3.1 34.5 1.0
OP3 D:DA7 3.1 54.5 1.0
CG A:ASP74 3.1 22.6 1.0
OD1 A:ASP74 3.3 24.1 1.0
OD2 A:ASP90 3.4 29.6 1.0
MN A:MN1004 3.4 48.2 1.0
C A:ILE91 3.5 24.0 1.0
OE1 A:GLU45 3.5 33.2 1.0
OP2 D:DA7 3.6 53.8 1.0
N A:ILE91 3.7 25.1 1.0
CA A:ILE91 4.0 25.6 1.0
CG A:ASP90 4.1 31.2 1.0
O5' D:DA7 4.2 51.5 1.0
O D:HOH312 4.2 37.9 1.0
CG A:GLU45 4.3 31.8 1.0
CB A:ILE91 4.3 27.9 1.0
O A:HOH1059 4.4 28.6 1.0
OD1 A:ASP90 4.5 35.2 1.0
CB A:ASP74 4.5 25.4 1.0
C5' D:DA7 4.6 46.5 1.0
C A:ASP90 4.6 25.7 1.0
CD A:LYS92 4.6 27.0 1.0
O A:HOH1186 4.7 31.3 1.0
N A:LYS92 4.7 23.4 1.0
NZ A:LYS92 4.7 29.1 1.0
C3' D:DA7 4.8 43.0 1.0
CE A:LYS92 4.8 26.9 1.0
CA A:ASP90 5.0 26.4 1.0

Manganese binding site 2 out of 6 in 1stx

Go back to Manganese Binding Sites List in 1stx
Manganese binding site 2 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1004

b:48.2
occ:1.00
 OP3 D:DA7 2.2 54.5 1.0
OD1 A:ASP74 2.2 24.1 1.0
OE1 A:GLU45 2.3 33.2 1.0
O A:HOH1187 2.4 32.5 1.0
O A:HOH1186 2.5 31.3 1.0
CG A:ASP74 3.1 22.6 1.0
CD A:GLU45 3.1 34.5 1.0
OE2 A:GLU45 3.2 34.5 1.0
MN A:MN1003 3.4 38.1 1.0
OD2 A:ASP74 3.5 22.4 1.0
P D:DA7 3.5 54.1 1.0
OP1 D:DA7 4.0 56.6 1.0
O D:HOH384 4.1 41.3 1.0
O5' D:DA7 4.4 51.5 1.0
C5' D:DA7 4.4 46.5 1.0
CB A:ASP74 4.4 25.4 1.0
OP2 D:DA7 4.5 53.8 1.0
O A:HOH1097 4.6 41.4 1.0
CG A:GLU45 4.6 31.8 1.0
OD2 B:ASP36 4.8 51.9 1.0
O A:HOH1134 4.9 32.8 1.0
CA A:ASP74 4.9 25.8 1.0

Manganese binding site 3 out of 6 in 1stx

Go back to Manganese Binding Sites List in 1stx
Manganese binding site 3 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1005

b:41.1
occ:1.00
 NE2 A:HIS71 2.2 32.9 1.0
OP1 F:DT11 2.4 39.8 1.0
O A:HOH1103 2.4 27.8 1.0
O A:HOH1133 2.5 23.4 1.0
CE1 A:HIS71 3.0 34.6 1.0
NE2 A:GLN68 3.3 45.0 1.0
CD2 A:HIS71 3.4 31.7 1.0
P F:DT11 3.8 33.6 1.0
CD A:GLN68 4.1 44.5 1.0
ND1 A:HIS71 4.2 34.3 1.0
C5' F:DT11 4.3 38.6 1.0
OE1 A:GLN68 4.3 45.6 1.0
O5' F:DT11 4.3 36.6 1.0
CG A:HIS71 4.4 32.6 1.0
N A:ASN120 4.4 22.2 1.0
O A:HOH1161 4.5 46.2 1.0
O3' F:DT10 4.5 35.0 1.0
O A:HOH1104 4.6 55.4 1.0
O A:THR118 4.6 25.9 1.0
CA A:ASN120 4.8 22.6 1.0
OP2 F:DT11 4.8 37.2 1.0
O A:HOH1081 4.9 45.7 1.0

Manganese binding site 4 out of 6 in 1stx

Go back to Manganese Binding Sites List in 1stx
Manganese binding site 4 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1007

b:64.1
occ:1.00
 O A:LYS102 1.9 37.6 1.0
NE2 A:HIS193 2.8 44.1 1.0
C A:LYS102 3.0 39.0 1.0
CD2 A:HIS193 3.5 41.6 1.0
CA A:LYS102 3.8 40.0 1.0
CB A:LYS102 3.8 40.5 1.0
CE1 A:HIS193 3.9 43.2 1.0
N A:ILE103 3.9 37.3 1.0
N A:LYS102 4.1 43.4 1.0
CA A:ILE103 4.1 35.5 1.0
O A:HOH1078 4.4 43.7 1.0
O A:HOH1030 4.4 50.8 1.0
CG A:GLU101 4.5 51.9 1.0
C A:ILE103 4.7 34.4 1.0
O A:HOH1060 4.7 25.0 1.0
OE2 A:GLU101 4.7 53.6 1.0
CG A:HIS193 4.7 39.5 1.0
O A:HOH1027 4.8 46.4 1.0
ND1 A:HIS193 4.9 41.5 1.0
C A:GLU101 4.9 47.1 1.0
N A:LYS104 5.0 33.6 1.0

Manganese binding site 5 out of 6 in 1stx

Go back to Manganese Binding Sites List in 1stx
Manganese binding site 5 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1002

b:38.4
occ:1.00
 OE1 B:GLU45 2.1 33.9 1.0
OD2 B:ASP74 2.2 30.1 1.0
OP2 F:DA7 2.3 48.7 1.0
O F:HOH276 2.3 35.8 1.0
O B:ILE91 2.4 25.5 1.0
CG B:ASP74 3.2 30.4 1.0
CD B:GLU45 3.2 36.5 1.0
P F:DA7 3.3 50.2 1.0
OP3 F:DA7 3.4 46.1 1.0
C B:ILE91 3.4 26.4 1.0
OD1 B:ASP74 3.4 33.8 1.0
O F:HOH63 3.6 16.9 1.0
N B:ILE91 3.6 26.9 1.0
OE2 B:GLU45 3.7 35.5 1.0
OD1 B:ASP90 3.7 27.1 1.0
CA B:ILE91 3.8 26.8 1.0
CB B:ILE91 3.9 28.5 1.0
CG B:ASP90 4.2 31.0 1.0
O5' F:DA7 4.3 47.3 1.0
OP1 F:DA7 4.4 49.8 1.0
CG B:GLU45 4.5 32.8 1.0
CB B:ASP74 4.5 29.8 1.0
C B:ASP90 4.5 26.5 1.0
OD2 B:ASP90 4.5 34.5 1.0
N B:LYS92 4.6 25.8 1.0
OP1 F:DT8 4.6 42.6 1.0
NZ B:LYS92 4.7 25.1 1.0
CG1 B:ILE91 4.7 29.9 1.0
O E:HOH277 4.8 29.1 1.0
O B:HOH1102 4.8 34.0 1.0
C5' F:DA7 4.8 44.4 1.0
CD B:LYS92 4.8 25.8 1.0
CA B:ASP90 5.0 27.3 1.0

Manganese binding site 6 out of 6 in 1stx

Go back to Manganese Binding Sites List in 1stx
Manganese binding site 6 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1006

b:51.0
occ:1.00
 NE2 B:HIS71 2.2 41.2 1.0
O B:HOH1108 2.4 18.6 1.0
OP1 D:DT11 2.5 44.8 1.0
O B:HOH1109 2.7 52.9 1.0
CE1 B:HIS71 2.9 43.0 1.0
CD2 B:HIS71 3.4 39.2 1.0
NE2 B:GLN68 3.9 53.1 1.0
OE1 B:GLN68 4.0 55.7 1.0
P D:DT11 4.0 45.5 1.0
ND1 B:HIS71 4.1 41.2 1.0
O B:THR118 4.3 33.3 1.0
N B:ASN120 4.3 30.0 1.0
CD B:GLN68 4.4 53.7 1.0
CG B:HIS71 4.4 39.4 1.0
O B:HOH1052 4.5 56.4 1.0
C5' D:DT11 4.6 46.9 1.0
O3' D:DT10 4.7 44.5 1.0
O5' D:DT11 4.7 44.0 1.0
CA B:ASN120 4.8 30.0 1.0

Reference:

N.C.Horton, J.J.Perona. Dna Cleavage By Ecorv Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites Biochemistry V. 43 6841 2004.
ISSN: ISSN 0006-2960
PubMed: 15170321
DOI: 10.1021/BI0499056
Page generated: Sat Oct 5 12:27:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy