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Manganese in PDB 1sx5: K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form

Enzymatic activity of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form

All present enzymatic activity of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form:
3.1.21.4;

Protein crystallography data

The structure of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form, PDB code: 1sx5 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 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.708, 48.627, 63.544, 96.68, 108.94, 107.33
R / Rfree (%) 21.4 / 25.4

Manganese Binding Sites:

The binding sites of Manganese atom in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form (pdb code 1sx5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form, PDB code: 1sx5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 1sx5

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Manganese binding site 1 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:24.5
occ:1.00
 O A:HOH503 2.0 31.1 1.0
OP2 D:DA7 2.1 22.8 1.0
OD1 A:ASP74 2.1 17.4 1.0
OE1 A:GLU45 2.3 23.0 1.0
O A:HOH530 2.7 33.3 1.0
CG A:ASP74 3.1 17.6 1.0
OP1 D:DA7 3.2 28.1 1.0
O B:HOH507 3.2 39.3 1.0
P D:DA7 3.2 24.8 1.0
CD A:GLU45 3.3 21.6 1.0
OE2 A:GLU45 3.6 25.1 1.0
OD2 A:ASP74 3.6 14.9 1.0
MN A:MN402 3.6 23.5 1.0
O A:HOH495 3.8 40.1 1.0
OD2 B:ASP36 4.1 33.4 1.0
CG B:ASP36 4.2 33.7 1.0
OP3 D:DA7 4.2 25.3 1.0
CB A:ASP74 4.2 16.9 1.0
O B:HOH504 4.3 30.7 1.0
O5' D:DA7 4.3 25.8 1.0
O A:HOH526 4.3 27.0 1.0
O A:HOH531 4.4 26.7 1.0
CB B:ASP36 4.5 31.0 1.0
O D:HOH238 4.5 22.2 1.0
OD1 B:ASP36 4.7 34.8 1.0
CG A:GLU45 4.7 22.3 1.0
CA A:ASP74 4.7 17.2 1.0
O B:HOH477 4.7 11.9 1.0
O D:HOH237 4.9 37.4 1.0

Manganese binding site 2 out of 9 in 1sx5

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Manganese binding site 2 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:23.5
occ:1.00
 O D:HOH238 1.9 22.2 1.0
OE2 A:GLU45 1.9 25.1 1.0
O D:HOH237 2.1 37.4 1.0
OP2 D:DA7 2.2 22.8 1.0
O A:ILE91 2.3 14.4 1.0
OD2 A:ASP74 2.3 14.9 1.0
CD A:GLU45 2.9 21.6 1.0
CG A:ASP74 3.2 17.6 1.0
OD1 A:ASP74 3.4 17.4 1.0
OE1 A:GLU45 3.4 23.0 1.0
C A:ILE91 3.4 14.1 1.0
P D:DA7 3.4 24.8 1.0
MN A:MN401 3.6 24.5 1.0
OP3 D:DA7 3.7 25.3 1.0
O5' D:DA7 3.7 25.8 1.0
N A:ILE91 3.7 13.8 1.0
CA A:ILE91 3.9 13.8 1.0
O D:HOH104 3.9 24.2 1.0
CB A:ILE91 4.1 15.1 1.0
CG A:GLU45 4.2 22.3 1.0
OD1 A:ASP90 4.2 18.3 1.0
O A:HOH530 4.2 33.3 1.0
N A:LYS92 4.5 13.2 1.0
CD A:LYS92 4.6 22.5 1.0
CB A:ASP74 4.6 16.9 1.0
OP1 D:DA7 4.7 28.1 1.0
CG A:ASP90 4.7 20.1 1.0
NZ A:LYS92 4.7 23.5 1.0
C A:ASP90 4.8 15.7 1.0
CA A:LYS92 4.9 15.3 1.0
OP1 D:DT8 4.9 31.6 1.0
O3' D:DA7 4.9 30.0 1.0
CE A:LYS92 4.9 19.2 1.0

Manganese binding site 3 out of 9 in 1sx5

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Manganese binding site 3 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:39.1
occ:1.00
 O A:HOH574 2.0 22.2 1.0
O A:HOH575 2.0 34.5 1.0
NE2 A:HIS193 2.1 23.4 1.0
O A:HOH474 2.4 43.7 1.0
CE1 A:HIS193 2.8 24.1 1.0
CD2 A:HIS193 3.3 23.8 1.0
ND1 A:HIS193 4.0 25.6 1.0
O A:LYS102 4.1 21.5 1.0
CG A:HIS193 4.2 22.4 1.0
CB A:LYS102 4.7 26.3 1.0
O A:HOH450 4.7 39.2 1.0
C A:LYS102 4.7 22.7 1.0

Manganese binding site 4 out of 9 in 1sx5

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Manganese binding site 4 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:35.3
occ:1.00
 O A:HOH420 2.1 27.2 1.0
ND1 A:HIS195 2.3 25.6 1.0
OD2 A:ASP198 2.3 23.0 1.0
CE1 A:HIS195 3.2 25.9 1.0
CG A:ASP198 3.2 21.4 1.0
CG A:HIS195 3.3 24.2 1.0
OD1 A:ASP198 3.5 24.3 1.0
CB A:HIS195 3.6 22.3 1.0
N A:HIS195 4.1 18.1 1.0
NE2 A:HIS195 4.4 26.5 1.0
CD2 A:HIS195 4.4 25.8 1.0
CA A:HIS195 4.5 19.2 1.0
CB A:ASP198 4.6 19.0 1.0
CB A:ALA194 4.9 18.1 1.0

Manganese binding site 5 out of 9 in 1sx5

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Manganese binding site 5 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:32.9
occ:1.00
 O A:HOH410 2.1 27.1 1.0
NE2 A:HIS71 2.3 25.6 1.0
O A:HOH411 2.3 30.6 1.0
OP1 F:DT11 2.4 36.9 1.0
CE1 A:HIS71 3.1 28.5 1.0
CD2 A:HIS71 3.3 25.0 1.0
P F:DT11 3.9 36.0 1.0
OE1 A:GLN68 3.9 40.5 1.0
ND1 A:HIS71 4.3 24.8 1.0
N A:ASN120 4.3 21.4 1.0
C5' F:DT11 4.4 43.9 1.0
CG A:HIS71 4.4 25.4 1.0
O5' F:DT11 4.5 40.3 1.0
O A:THR118 4.6 25.2 1.0
O3' F:DT10 4.6 34.0 1.0
CA A:ASN120 4.7 22.2 1.0
OP2 F:DT11 4.9 37.3 1.0
CD A:GLN68 4.9 38.6 1.0

Manganese binding site 6 out of 9 in 1sx5

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Manganese binding site 6 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn405

b:23.5
occ:1.00
 O B:ILE91 2.2 13.8 1.0
OP1 F:DA7 2.2 34.9 1.0
OP3 F:DA7 2.2 28.8 1.0
OD2 B:ASP74 2.3 16.9 1.0
OD2 B:ASP90 2.4 22.7 1.0
P F:DA7 2.7 31.6 1.0
C B:ILE91 3.2 16.0 1.0
CG B:ASP74 3.2 16.7 1.0
CG B:ASP90 3.3 18.8 1.0
N B:ILE91 3.5 16.2 1.0
OD1 B:ASP74 3.5 17.1 1.0
O5' F:DA7 3.5 34.0 1.0
OE2 B:GLU45 3.7 30.9 1.0
OD1 B:ASP90 3.7 17.3 1.0
CA B:ILE91 3.8 15.2 1.0
MN B:MN408 3.8 36.9 1.0
OP2 F:DA7 4.0 32.6 1.0
O B:HOH558 4.0 13.5 1.0
CB B:ILE91 4.1 18.2 1.0
O B:HOH512 4.1 31.9 1.0
CD B:LYS92 4.2 19.8 1.0
NZ B:LYS92 4.2 22.0 1.0
C B:ASP90 4.3 16.6 1.0
N B:LYS92 4.4 16.0 1.0
O B:HOH561 4.4 50.2 1.0
CE B:LYS92 4.5 21.4 1.0
CB B:ASP90 4.5 18.1 1.0
CB B:ASP74 4.6 16.2 1.0
O B:HOH445 4.7 25.9 1.0
O B:HOH413 4.7 35.7 1.0
C5' F:DA7 4.7 33.1 1.0
CA B:ASP90 4.7 16.3 1.0
CA B:LYS92 4.8 17.7 1.0
C3' F:DA7 4.9 31.6 1.0
CD B:GLU45 4.9 31.9 1.0
C4' F:DA7 4.9 32.7 1.0
CG1 B:ILE91 4.9 21.9 1.0

Manganese binding site 7 out of 9 in 1sx5

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Manganese binding site 7 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn406

b:24.7
occ:1.00
 O D:HOH37 1.9 40.6 1.0
O D:HOH163 2.2 24.3 1.0
NE2 B:HIS71 2.2 22.3 1.0
OP1 D:DT11 2.2 26.2 1.0
O B:HOH476 2.3 24.4 1.0
O B:HOH423 2.5 24.7 1.0
CE1 B:HIS71 3.1 25.8 1.0
CD2 B:HIS71 3.2 22.1 1.0
P D:DT11 3.7 26.2 1.0
C5' D:DT11 4.0 30.9 1.0
ND1 B:HIS71 4.3 23.5 1.0
O5' D:DT11 4.3 25.8 1.0
O3' D:DT10 4.3 23.6 1.0
CG B:HIS71 4.3 23.4 1.0
O B:THR118 4.4 24.6 1.0
N B:ASN120 4.4 19.5 1.0
OP2 D:DT11 4.7 25.8 1.0
CA B:ASN120 4.8 19.7 1.0
O B:ILE121 4.9 18.2 1.0

Manganese binding site 8 out of 9 in 1sx5

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Manganese binding site 8 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn407

b:60.5
occ:1.00
 ND1 B:HIS195 2.4 35.9 1.0
OD2 B:ASP198 2.4 32.7 1.0
CG B:ASP198 3.3 30.2 1.0
CE1 B:HIS195 3.3 35.6 1.0
CG B:HIS195 3.4 34.3 1.0
OD1 B:ASP198 3.4 32.3 1.0
CB B:HIS195 3.7 31.7 1.0
N B:HIS195 4.0 28.2 1.0
CA B:HIS195 4.4 28.9 1.0
NE2 B:HIS195 4.4 35.7 1.0
CD2 B:HIS195 4.5 34.1 1.0
CB B:ASP198 4.7 26.2 1.0

Manganese binding site 9 out of 9 in 1sx5

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Manganese binding site 9 out of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn408

b:36.9
occ:1.00
 OE2 B:GLU45 2.0 30.9 1.0
OD1 B:ASP74 2.3 17.1 1.0
O B:HOH559 2.4 34.1 1.0
O B:HOH558 2.4 13.5 1.0
CD B:GLU45 2.6 31.9 1.0
OE1 B:GLU45 2.8 35.9 1.0
CG B:ASP74 3.2 16.7 1.0
OP1 F:DA7 3.2 34.9 1.0
OD2 B:ASP74 3.6 16.9 1.0
O5' F:DA7 3.6 34.0 1.0
MN B:MN405 3.8 23.5 1.0
CG B:GLU45 3.9 29.0 1.0
P F:DA7 4.1 31.6 1.0
CB B:ASP74 4.4 16.2 1.0
O B:HOH560 4.4 49.6 1.0
O A:HOH412 4.6 34.7 1.0
OD2 A:ASP36 4.6 42.5 1.0
O B:HOH491 4.6 28.8 1.0
C5' F:DA7 4.9 33.1 1.0
CB B:GLU45 4.9 21.4 1.0
OP3 F:DA7 4.9 28.8 1.0
CA B:ASP74 5.0 15.3 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: Tue Dec 15 03:55:42 2020

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