Atomistry » Manganese » PDB 6dkt-6e4c » 6dpk
Atomistry »
  Manganese »
    PDB 6dkt-6e4c »
      6dpk »

Manganese in PDB 6dpk: Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C, PDB code: 6dpk was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.492, 37.598, 61.734, 90.00, 96.79, 90.00
R / Rfree (%) 14.3 / 16.9

Other elements in 6dpk:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C also contains other interesting chemical elements:

Potassium (K) 2 atoms
Iodine (I) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C (pdb code 6dpk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C, PDB code: 6dpk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6dpk

Go back to Manganese Binding Sites List in 6dpk
Manganese binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:24.7
occ:0.40
OE1 A:GLU166 2.1 27.3 1.0
O A:HOH304 2.1 24.3 0.5
O A:HOH412 2.2 31.1 1.0
O A:HOH414 2.2 32.4 0.5
OD1 A:ASP163 2.6 26.9 1.0
O A:HOH317 2.8 39.8 1.0
CD A:GLU166 3.1 23.3 1.0
HH22 A:ARG151 3.2 41.0 1.0
HA A:ASP163 3.3 22.6 1.0
OE2 A:GLU166 3.4 24.8 1.0
NZ A:LYS144 3.5 77.7 1.0
CG A:ASP163 3.6 30.5 1.0
HH21 A:ARG151 3.8 41.0 1.0
NH2 A:ARG151 3.8 34.1 1.0
O A:HOH362 3.9 38.3 1.0
CA A:ASP163 4.2 18.8 1.0
HB2 A:GLU166 4.2 22.8 1.0
CB A:ASP163 4.3 20.3 1.0
HZ3 A:TRP159 4.3 28.7 1.0
HB3 A:ASP163 4.3 24.4 1.0
OD2 A:ASP163 4.4 30.1 1.0
CG A:GLU166 4.4 18.6 1.0
HG12 A:VAL162 4.4 23.2 1.0
O A:HOH367 4.7 43.7 1.0
CB A:GLU166 4.7 19.0 1.0
CE A:LYS144 4.8 83.3 1.0
HG3 A:GLU166 4.8 22.3 1.0
HB3 A:GLU166 4.8 22.8 1.0
CD A:LYS144 4.9 63.0 1.0
N A:ASP163 4.9 17.3 1.0

Manganese binding site 2 out of 4 in 6dpk

Go back to Manganese Binding Sites List in 6dpk
Manganese binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn214

b:18.0
occ:1.00
OD2 A:ASP71 2.1 17.5 1.0
O A:HOH348 2.1 20.0 1.0
O b:HOH201 2.1 19.1 0.6
OD1 A:ASP192 2.1 22.3 1.0
OP3 b:C5 2.1 39.1 0.4
O A:HOH316 2.2 19.2 1.0
OP1 b:C5 2.2 20.1 0.4
OP1 b:C5 2.3 17.9 0.4
OP1 b:C5 2.3 15.5 0.2
P b:C5 2.8 15.6 0.4
CG A:ASP71 3.1 15.6 1.0
HA A:ASP192 3.1 22.4 1.0
CG A:ASP192 3.2 20.5 1.0
P b:C5 3.4 32.2 0.4
P b:C5 3.5 15.1 0.2
OD1 A:ASP71 3.5 15.4 1.0
H A:TYR193 3.5 25.0 1.0
HB2 A:ASP192 3.7 24.3 1.0
OP2 b:C5 3.8 15.9 0.4
CB A:ASP192 3.8 20.2 1.0
MN A:MN215 3.8 16.9 1.0
O A:HOH387 3.9 24.4 1.0
OP2 b:C5 3.9 24.0 0.4
CA A:ASP192 3.9 18.7 1.0
OP2 b:C5 3.9 17.8 0.2
MN b:MN101 3.9 26.2 0.4
O5' b:C5 3.9 15.3 0.4
OP2 b:G6 3.9 21.7 1.0
OD2 A:ASP132 4.1 24.5 1.0
O A:VAL72 4.1 17.1 1.0
O5' b:C5 4.1 16.1 0.2
HG22 A:ILE189 4.1 20.8 1.0
O5' b:C5 4.1 20.8 0.4
OD2 A:ASP192 4.2 25.0 1.0
O b:HOH205 4.2 28.1 0.4
OE2 A:GLU188 4.3 30.6 1.0
N A:TYR193 4.3 20.8 1.0
C5' b:C5 4.3 19.2 1.0
CB A:ASP71 4.5 15.0 1.0
HB3 A:ASP71 4.5 18.1 1.0
OP3 b:C5 4.6 23.1 0.4
C A:ASP192 4.7 20.1 1.0
O A:HOH308 4.7 17.9 0.2
HD1 A:TYR193 4.7 21.8 1.0
HB3 A:ASP192 4.7 24.3 1.0
HG21 A:ILE189 4.7 20.8 1.0
O3' B:U4 4.8 14.5 0.2
HB2 A:ASP71 4.8 18.1 1.0
CG2 A:ILE189 4.8 17.4 1.0
O A:HOH312 4.8 47.5 1.0
HB2 A:TYR193 4.9 26.7 1.0
HG23 A:ILE189 4.9 20.8 1.0
N A:ASP192 5.0 16.8 1.0

Manganese binding site 3 out of 4 in 6dpk

Go back to Manganese Binding Sites List in 6dpk
Manganese binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn215

b:16.9
occ:1.00
OP1 b:C5 2.1 17.9 0.4
OE1 A:GLU109 2.1 16.5 1.0
OD1 A:ASP71 2.1 15.4 1.0
OD1 A:ASP132 2.1 17.4 1.0
OP1 b:C5 2.1 15.5 0.2
OP1 b:C5 2.1 20.1 0.4
OP3 b:C5 2.5 23.1 0.4
O3' B:U4 2.6 14.5 0.2
CG A:ASP132 2.8 17.9 1.0
OD2 A:ASP132 2.8 24.5 1.0
P b:C5 2.8 32.2 0.4
P b:C5 2.9 15.1 0.2
CD A:GLU109 3.0 16.8 1.0
CG A:ASP71 3.1 15.6 1.0
OE2 A:GLU109 3.3 16.7 1.0
C3' B:U4 3.4 21.9 0.4
P b:C5 3.4 15.6 0.4
O3' B:U4 3.5 17.5 0.4
O A:HOH335 3.5 17.5 1.0
HG12 A:VAL72 3.5 18.1 1.0
OD2 A:ASP71 3.6 17.5 1.0
H A:VAL72 3.8 17.9 1.0
MN A:MN214 3.8 18.0 1.0
O5' b:C5 3.9 20.8 0.4
C3' B:U4 3.9 18.3 0.2
C5' b:C5 3.9 19.2 1.0
O5' b:C5 3.9 16.1 0.2
OP2 b:C5 4.0 15.9 0.4
OP2 b:C5 4.0 17.8 0.2
O A:HOH348 4.0 20.0 1.0
OP2 b:C5 4.0 24.0 0.4
O5' b:C5 4.1 15.3 0.4
HA A:ASP71 4.1 16.1 1.0
CB A:ASP132 4.2 16.1 1.0
H A:ASP132 4.2 17.8 1.0
C4' B:U4 4.3 33.2 0.2
HB2 A:SER133 4.3 22.2 1.0
CB A:ASP71 4.4 15.0 1.0
CG A:GLU109 4.4 14.1 1.0
C4' B:U4 4.4 18.1 0.4
OP3 b:C5 4.4 39.1 0.4
C5' B:U4 4.4 18.4 0.2
C2' B:U4 4.5 14.3 0.4
HG21 A:ILE189 4.5 20.8 1.0
CG1 A:VAL72 4.5 15.1 1.0
HG3 A:GLU109 4.5 16.9 1.0
N A:VAL72 4.6 14.9 1.0
O2' B:U4 4.6 14.1 0.2
C5' B:U4 4.6 15.4 0.4
O b:HOH201 4.6 19.1 0.6
HB2 A:ASP132 4.7 19.4 1.0
HB2 A:ASP71 4.7 18.1 1.0
CA A:ASP71 4.7 13.4 1.0
O2' B:U4 4.7 19.3 0.4
HG2 A:GLU109 4.7 16.9 1.0
HB3 A:ASP132 4.7 19.4 1.0
HG13 A:VAL72 4.8 18.1 1.0
C A:ASP132 4.8 16.4 1.0
K A:K216 4.8 18.7 0.4
C2' B:U4 4.8 23.9 0.2
CA A:ASP132 4.8 15.3 1.0
O A:VAL72 4.8 17.1 1.0
HG11 A:VAL72 4.9 18.1 1.0
N A:ASP132 4.9 14.8 1.0
O A:HOH316 4.9 19.2 1.0
HG22 A:ILE189 4.9 20.8 1.0
N A:SER133 5.0 16.5 1.0

Manganese binding site 4 out of 4 in 6dpk

Go back to Manganese Binding Sites List in 6dpk
Manganese binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mn101

b:26.2
occ:0.40
O b:HOH201 2.1 19.1 0.6
O b:HOH207 2.2 26.1 0.4
O A:HOH387 2.2 24.4 1.0
O A:HOH301 2.2 28.0 0.4
OP3 b:C5 2.3 39.1 0.4
O b:HOH205 2.3 28.1 0.4
OP2 b:G6 2.4 21.7 1.0
P b:C5 3.4 15.6 0.4
O A:HOH312 3.5 47.5 1.0
O A:ARG195 3.5 54.4 0.5
O5' b:G6 3.6 20.4 1.0
P b:G6 3.6 19.3 1.0
O5' b:C5 3.7 15.3 0.4
O A:HOH316 3.9 19.2 1.0
MN A:MN214 3.9 18.0 1.0
OP2 b:C5 3.9 15.9 0.4
OD1 A:ASP192 3.9 22.3 1.0
O5' b:C5 4.0 16.1 0.2
OP2 b:C5 4.0 24.0 0.4
OP2 b:C5 4.0 17.8 0.2
O5' b:C5 4.1 20.8 0.4
C A:ARG195 4.1 51.3 0.5
P b:C5 4.4 15.1 0.2
P b:C5 4.4 32.2 0.4
OP1 b:C5 4.5 20.1 0.4
OP1 b:C5 4.5 15.5 0.2
C3' b:C5 4.5 17.1 1.0
OP1 b:C5 4.5 17.9 0.4
O b:HOH202 4.6 43.0 1.0
O3' b:C5 4.6 17.8 1.0
C5' b:C5 4.6 19.2 1.0
OP1 b:G6 4.7 19.4 1.0
C5' b:G6 4.9 22.5 1.0
N A:ARG195 4.9 75.0 0.5
CG A:ASP192 4.9 20.5 1.0
O b:HOH204 5.0 35.9 1.0
O A:HOH348 5.0 20.0 1.0

Reference:

N.L.Samara, W.Yang. Cation Trafficking Propels Rna Hydrolysis. Nat. Struct. Mol. Biol. V. 25 715 2018.
ISSN: ESSN 1545-9985
PubMed: 30076410
DOI: 10.1038/S41594-018-0099-4
Page generated: Sun Oct 6 04:10:02 2024

Last articles

Mg in 1MZY
Mg in 1MZP
Mg in 1MXG
Mg in 1MXC
Mg in 1MXB
Mg in 1MXA
Mg in 1MWM
Mg in 1MUW
Mg in 1MV5
Mg in 1MUM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy