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Manganese in PDB 1xhv: Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+

Enzymatic activity of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+

All present enzymatic activity of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+:
3.1.21.4;

Protein crystallography data

The structure of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+, PDB code: 1xhv was solved by C.Etzkorn, N.C.Horton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.800, 178.200, 257.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 27.4

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Manganese atom in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ (pdb code 1xhv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 22 binding sites of Manganese where determined in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+, PDB code: 1xhv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 22 in 1xhv

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Manganese binding site 1 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1102

b:56.0
occ:1.00
 O E:HOH1078 2.4 33.4 1.0
OD2 B:ASP114 2.5 36.0 1.0
O B:HOH1158 2.6 31.2 1.0
O B:HOH1157 2.7 37.5 1.0
OP3 F:DG8 2.9 53.7 1.0
O3' E:DC7 2.9 41.8 1.0
O B:HOH1333 3.0 14.7 1.0
O5' F:DG8 3.4 59.3 1.0
P F:DG8 3.4 61.8 1.0
OP2 F:DG8 3.4 56.1 1.0
CG B:ASP114 3.4 38.5 1.0
C3' E:DC7 3.5 21.9 1.0
O B:HOH1290 3.6 31.6 1.0
OD1 B:ASP114 3.8 37.9 1.0
OD2 B:ASP127 3.9 55.9 1.0
MN B:MN1101 4.0 63.4 1.0
C5' F:DG8 4.0 47.6 1.0
O B:ASP111 4.2 32.0 1.0
O B:HOH1430 4.4 26.2 1.0
C4' E:DC7 4.4 29.9 1.0
O B:HOH1429 4.6 59.4 1.0
CG B:ASP127 4.6 51.3 1.0
C2' E:DC7 4.7 40.0 1.0
CB B:ASP114 4.7 36.9 1.0
O F:HOH97 4.7 58.1 1.0
N B:ASP114 4.8 35.8 1.0
OD1 B:ASP127 4.8 56.7 1.0
O F:HOH1079 4.9 57.2 1.0
CA B:ASP114 4.9 32.8 1.0
OP1 F:DG8 4.9 60.2 1.0
C B:ALA113 4.9 33.3 1.0
O B:THR112 5.0 27.3 1.0

Manganese binding site 2 out of 22 in 1xhv

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Manganese binding site 2 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1121

b:94.9
occ:1.00
 OP1 F:DG8 2.8 60.2 1.0
O B:HOH1331 2.9 48.5 1.0
MN B:MN1128 3.0 0.6 1.0
O B:HOH1332 3.1 56.5 1.0
OP3 F:DG8 3.4 53.7 1.0
O B:HOH1422 3.4 71.4 1.0
P F:DG8 3.6 61.8 1.0
OE1 B:GLU35 3.7 82.2 1.0
O B:HOH1429 3.9 59.4 1.0
O A:HOH1114 4.0 64.2 1.0
OE2 B:GLU107 4.2 69.1 1.0
O F:HOH422 4.2 33.3 1.0
O A:HOH1317 4.2 0.8 1.0
O B:HOH1428 4.3 46.6 1.0
OP2 F:DG8 4.3 56.1 1.0
CD B:GLU107 4.5 65.3 1.0
CD B:GLU35 4.6 78.2 1.0
O B:HOH1290 4.7 31.6 1.0
CG B:GLU107 4.7 57.5 1.0
OE2 B:GLU35 4.9 81.6 1.0
O5' F:DG8 4.9 59.3 1.0

Manganese binding site 3 out of 22 in 1xhv

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Manganese binding site 3 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1120

b:70.6
occ:1.00
 O F:HOH1031 2.8 51.8 1.0
N7 G:DG1 2.9 27.8 1.0
C8 G:DG1 3.8 31.2 1.0
N4 G:DC2 3.8 29.1 1.0
O6 G:DG1 3.9 25.7 1.0
C5 G:DG1 3.9 20.2 1.0
O F:HOH138 4.2 46.4 1.0
C6 G:DG1 4.3 19.8 1.0
O F:HOH1032 4.3 47.0 1.0
O5' G:DG1 4.6 47.3 1.0
C4 G:DC2 4.7 30.8 1.0
C5 G:DC2 4.8 32.6 1.0
N9 G:DG1 5.0 32.1 1.0

Manganese binding site 4 out of 22 in 1xhv

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Manganese binding site 4 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1109

b:37.5
occ:1.00
 O3' G:DC7 2.3 23.3 1.0
O A:HOH1128 2.3 33.7 1.0
OD2 A:ASP114 2.4 37.1 1.0
OP2 H:DG8 2.4 33.5 1.0
O A:HOH1224 2.5 41.1 1.0
O A:HOH1201 2.6 28.5 1.0
CG A:ASP114 3.3 30.1 1.0
P H:DG8 3.4 27.1 1.0
OP1 H:DG8 3.6 43.0 1.0
C3' G:DC7 3.6 22.8 1.0
O5' H:DG8 3.6 27.8 1.0
OD2 A:ASP127 3.7 53.6 1.0
OD1 A:ASP114 3.7 32.0 1.0
O H:HOH957 3.9 25.2 1.0
O G:HOH1085 4.0 38.2 1.0
MN A:MN1103 4.1 43.0 1.0
O A:ASP111 4.2 38.4 1.0
C5' H:DG8 4.2 34.3 1.0
C4' G:DC7 4.3 31.7 1.0
C2' G:DC7 4.4 30.2 1.0
CG A:ASP127 4.5 50.0 1.0
OD1 A:ASP127 4.5 52.4 1.0
CB A:ASP114 4.6 33.2 1.0
N A:ASP114 4.6 33.4 1.0
CA A:ASP114 4.7 30.4 1.0
O A:HOH1223 4.7 49.1 1.0
OP3 H:DG8 4.8 39.1 1.0
C A:ALA113 4.9 33.0 1.0
MN H:MN1126 4.9 80.5 1.0
O A:HOH1315 5.0 46.0 1.0

Manganese binding site 5 out of 22 in 1xhv

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Manganese binding site 5 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1126

b:80.5
occ:1.00
 OE2 A:GLU38 2.4 55.5 1.0
OP1 H:DG8 2.5 43.0 1.0
O H:HOH967 3.0 64.7 1.0
P H:DG8 3.2 27.1 1.0
OP3 H:DG8 3.3 39.1 1.0
OE1 A:GLU107 3.5 73.7 1.0
CD A:GLU38 3.6 46.0 1.0
OP2 H:DG8 3.6 33.5 1.0
OD2 A:ASP114 3.6 37.1 1.0
O A:HOH1225 3.7 43.8 1.0
O H:HOH1325 3.8 39.0 1.0
OE1 A:GLU38 4.2 46.9 1.0
MN A:MN1103 4.2 43.0 1.0
CG A:ASP114 4.2 30.1 1.0
O A:HOH1223 4.3 49.1 1.0
O A:HOH1154 4.4 71.2 1.0
CD A:GLU107 4.5 71.3 1.0
O A:HOH1315 4.5 46.0 1.0
O A:HOH1115 4.6 53.0 1.0
MN H:MN1127 4.6 0.4 1.0
CG A:GLU38 4.7 37.6 1.0
NZ A:LYS55 4.7 73.5 1.0
O5' H:DG8 4.7 27.8 1.0
CB A:ASP114 4.8 33.2 1.0
OD1 A:ASP114 4.9 32.0 1.0
MN H:MN1109 4.9 37.5 1.0

Manganese binding site 6 out of 22 in 1xhv

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Manganese binding site 6 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1127

b:0.4
occ:1.00
 OP3 H:DG8 2.2 39.1 1.0
O H:HOH1325 2.5 39.0 1.0
O A:HOH1321 3.5 35.6 1.0
O H:HOH967 3.6 64.7 1.0
CA B:GLY30 3.6 0.5 1.0
P H:DG8 3.7 27.1 1.0
N B:GLY30 4.1 99.8 1.0
C B:GLY30 4.3 0.4 1.0
OP2 H:DG8 4.3 33.5 1.0
O H:HOH1327 4.3 64.8 1.0
O5' H:DG8 4.4 27.8 1.0
C5' H:DG8 4.5 34.3 1.0
OP1 H:DG8 4.6 43.0 1.0
MN H:MN1126 4.6 80.5 1.0
O B:GLY30 4.7 96.0 1.0
C4' H:DG8 4.8 37.1 1.0
N B:HIS31 4.9 0.9 1.0

Manganese binding site 7 out of 22 in 1xhv

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Manganese binding site 7 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1108

b:73.3
occ:1.00
 O J:HOH716 3.1 38.1 1.0
N7 J:DG12 3.9 37.2 1.0
C8 J:DG12 4.1 34.8 1.0
O K:HOH353 4.5 67.7 1.0
C5 J:DG12 4.7 30.7 1.0
O K:HOH713 4.7 40.4 1.0

Manganese binding site 8 out of 22 in 1xhv

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Manganese binding site 8 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1124

b:80.8
occ:1.00
 OE2 D:GLU38 2.3 78.0 1.0
OP1 J:DG8 2.3 34.5 1.0
O J:HOH306 2.4 38.4 1.0
OD2 D:ASP114 2.9 46.6 1.0
OP3 J:DG8 3.0 39.2 1.0
P J:DG8 3.1 37.5 1.0
CD D:GLU38 3.3 77.1 1.0
O D:HOH1140 3.3 45.4 1.0
O D:HOH1310 3.4 65.5 1.0
OE1 D:GLU38 3.6 70.8 1.0
OP2 J:DG8 3.8 39.5 1.0
CG D:ASP114 3.9 37.7 1.0
MN D:MN1114 4.0 51.9 1.0
O J:HOH309 4.3 57.5 1.0
OE2 D:GLU35 4.4 97.3 1.0
MN J:MN1125 4.4 92.8 1.0
O5' J:DG8 4.5 35.1 1.0
CB D:ASP114 4.5 41.7 1.0
CG D:GLU38 4.6 73.7 1.0
OD1 D:ASP114 4.7 39.2 1.0
OE1 D:GLU35 4.7 96.5 1.0
O D:HOH1142 4.8 61.5 1.0
MN D:MN1115 4.8 44.6 1.0
CD D:GLU35 5.0 95.0 1.0

Manganese binding site 9 out of 22 in 1xhv

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Manganese binding site 9 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1125

b:92.8
occ:1.00
 OP3 J:DG8 2.3 39.2 1.0
O J:HOH996 2.5 67.8 1.0
O D:HOH1310 2.7 65.5 1.0
O D:HOH1303 2.9 60.2 1.0
O J:HOH309 3.0 57.5 1.0
O D:HOH1302 3.3 48.1 1.0
P J:DG8 3.6 37.5 1.0
OE1 D:GLU35 3.8 96.5 1.0
O5' J:DG8 3.9 35.1 1.0
O J:HOH306 4.1 38.4 1.0
O J:HOH330 4.2 57.7 1.0
C5' J:DG8 4.2 34.9 1.0
O J:HOH995 4.3 53.4 1.0
OP1 J:DG8 4.4 34.5 1.0
MN J:MN1124 4.4 80.8 1.0
OP2 J:DG8 4.8 39.5 1.0
C4' J:DG8 4.9 40.7 1.0
CD D:GLU35 4.9 95.0 1.0

Manganese binding site 10 out of 22 in 1xhv

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Manganese binding site 10 out of 22 in the Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Hincii Bound to Cleaved Cognate Dna Gtcgac and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mn1122

b:0.2
occ:1.00
 O L:HOH1062 2.5 37.4 1.0
OP2 L:DG8 2.6 47.3 1.0
OP1 L:DG8 2.8 58.7 1.0
MN L:MN1123 3.1 0.2 1.0
OE2 C:GLU38 3.1 51.0 1.0
P L:DG8 3.2 53.4 1.0
CD C:GLU38 3.8 58.4 1.0
O L:HOH1008 4.0 87.7 1.0
O C:HOH1271 4.0 58.1 1.0
O5' L:DG8 4.3 41.7 1.0
OE1 C:GLU38 4.3 57.0 1.0
O L:HOH990 4.3 47.5 1.0
CB C:GLU35 4.4 71.6 1.0
OP3 L:DG8 4.5 52.2 1.0
CG C:GLU38 4.7 60.4 1.0
O C:HOH1270 4.8 36.1 1.0
CA C:GLU35 5.0 73.4 1.0

Reference:

C.Etzkorn, N.C.Horton. Mechanistic Insights From the Structures of Hincii Bound to Cognate Dna Cleaved From Addition of Mg(2+) and Mn(2+) J.Mol.Biol. V. 343 833 2004.
ISSN: ISSN 0022-2836
PubMed: 15476804
DOI: 10.1016/J.JMB.2004.08.082
Page generated: Sat Oct 5 13:01:40 2024

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