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Manganese in PDB 4peg: DBR1 in Complex with Guanosine-5'-Monophosphate

Protein crystallography data

The structure of DBR1 in Complex with Guanosine-5'-Monophosphate, PDB code: 4peg was solved by E.J.Montemayor, A.Katolik, N.E.Clark, A.B.Taylor, J.P.Schuermann, D.J.Combs, R.Johnsson, S.P.Holloway, S.W.Stevens, M.J.Damha, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.54 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.831, 141.499, 212.942, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.9

Manganese Binding Sites:

The binding sites of Manganese atom in the DBR1 in Complex with Guanosine-5'-Monophosphate (pdb code 4peg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the DBR1 in Complex with Guanosine-5'-Monophosphate, PDB code: 4peg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 4peg

Go back to Manganese Binding Sites List in 4peg
Manganese binding site 1 out of 5 in the DBR1 in Complex with Guanosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of DBR1 in Complex with Guanosine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:25.2
occ:1.00
OD1 A:ASN90 2.2 18.9 1.0
OD2 A:ASP45 2.2 29.3 1.0
NE2 A:HIS180 2.3 18.6 1.0
O A:HOH629 2.3 27.6 1.0
O2P A:5GP402 2.4 34.9 1.0
ND1 A:HIS230 2.5 19.9 1.0
CG A:ASP45 3.1 25.2 1.0
CG A:ASN90 3.2 20.1 1.0
CE1 A:HIS230 3.2 19.6 1.0
CE1 A:HIS180 3.3 20.3 1.0
O3P A:5GP402 3.3 42.0 1.0
CD2 A:HIS180 3.3 18.4 1.0
P A:5GP402 3.4 35.1 1.0
OD1 A:ASP45 3.4 23.2 1.0
ND2 A:ASN90 3.6 21.9 1.0
CG A:HIS230 3.7 22.6 1.0
CA A:HIS230 3.8 30.1 1.0
CB A:HIS230 4.1 25.4 1.0
CD2 A:HIS91 4.2 25.9 1.0
O5' A:5GP402 4.3 53.2 1.0
O A:HIS230 4.3 32.1 1.0
SG A:CYS14 4.4 30.7 0.5
ND1 A:HIS180 4.4 15.1 1.0
CG A:HIS180 4.4 16.6 1.0
NE2 A:HIS230 4.5 18.9 1.0
N A:ASN90 4.5 20.3 1.0
CB A:ASP45 4.5 25.3 1.0
CB A:ASN90 4.5 20.0 1.0
O1P A:5GP402 4.6 34.8 1.0
C A:HIS230 4.6 30.2 1.0
NE2 A:HIS91 4.7 18.7 1.0
C5' A:5GP402 4.7 52.8 1.0
N A:HIS230 4.7 33.6 1.0
CD2 A:HIS230 4.7 20.3 1.0

Manganese binding site 2 out of 5 in 4peg

Go back to Manganese Binding Sites List in 4peg
Manganese binding site 2 out of 5 in the DBR1 in Complex with Guanosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of DBR1 in Complex with Guanosine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:23.5
occ:1.00
OD1 B:ASN90 2.1 20.1 1.0
O2P B:5GP402 2.2 39.1 1.0
NE2 B:HIS180 2.3 18.1 1.0
ND1 B:HIS230 2.3 21.7 1.0
OD2 B:ASP45 2.4 24.3 1.0
O B:HOH626 2.4 25.1 1.0
CE1 B:HIS230 3.1 22.0 1.0
CG B:ASP45 3.2 18.5 1.0
CG B:ASN90 3.2 21.2 1.0
CE1 B:HIS180 3.2 20.4 1.0
CD2 B:HIS180 3.3 16.3 1.0
OD1 B:ASP45 3.4 21.3 1.0
P B:5GP402 3.4 40.9 1.0
CG B:HIS230 3.5 22.3 1.0
O1P B:5GP402 3.6 39.3 1.0
ND2 B:ASN90 3.6 21.0 1.0
CA B:HIS230 3.7 27.1 1.0
CB B:HIS230 3.9 23.4 1.0
O B:HIS230 4.2 25.5 1.0
O5' B:5GP402 4.3 51.6 1.0
NE2 B:HIS230 4.3 24.6 1.0
ND1 B:HIS180 4.3 18.1 1.0
C5' B:5GP402 4.3 57.8 1.0
SG B:CYS14 4.4 26.6 0.3
CG B:HIS180 4.4 15.3 1.0
O3P B:5GP402 4.5 43.0 1.0
N B:ASN90 4.5 18.7 1.0
CD2 B:HIS230 4.5 23.3 1.0
CB B:ASN90 4.5 24.5 1.0
CD2 B:HIS91 4.5 24.9 1.0
C B:HIS230 4.5 24.5 1.0
CB B:ASP45 4.5 16.0 1.0
N B:HIS230 4.6 30.6 1.0
SG B:CYS14 4.8 64.9 0.7
NE2 B:HIS91 4.9 25.4 1.0

Manganese binding site 3 out of 5 in 4peg

Go back to Manganese Binding Sites List in 4peg
Manganese binding site 3 out of 5 in the DBR1 in Complex with Guanosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of DBR1 in Complex with Guanosine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:24.8
occ:1.00
NE2 C:HIS180 2.2 21.2 1.0
OD1 C:ASN90 2.2 20.3 1.0
O C:HOH663 2.3 31.1 1.0
OD2 C:ASP45 2.3 27.6 1.0
ND1 C:HIS230 2.4 25.9 1.0
O2P C:5GP402 2.5 40.1 1.0
CE1 C:HIS230 3.1 28.9 1.0
CD2 C:HIS180 3.1 24.1 1.0
CE1 C:HIS180 3.1 22.9 1.0
CG C:ASP45 3.2 23.3 1.0
CG C:ASN90 3.2 20.9 1.0
O1P C:5GP402 3.4 39.6 1.0
OD1 C:ASP45 3.4 22.0 1.0
P C:5GP402 3.4 41.5 1.0
CG C:HIS230 3.5 25.4 1.0
ND2 C:ASN90 3.6 24.0 1.0
CA C:HIS230 3.8 30.4 1.0
CB C:HIS230 4.0 25.6 1.0
ND1 C:HIS180 4.2 22.0 1.0
C5' C:5GP402 4.3 57.3 1.0
CG C:HIS180 4.3 21.8 1.0
O C:HIS230 4.3 27.3 1.0
NE2 C:HIS230 4.3 28.7 1.0
O5' C:5GP402 4.3 56.3 1.0
N C:ASN90 4.5 23.3 1.0
CB C:ASN90 4.5 21.5 1.0
CB C:ASP45 4.5 25.9 1.0
CD2 C:HIS230 4.6 25.6 1.0
C C:HIS230 4.6 29.0 1.0
O3P C:5GP402 4.6 40.0 1.0
CD2 C:HIS91 4.7 26.3 1.0
N C:HIS230 4.7 32.4 1.0
NE2 C:HIS91 5.0 26.9 1.0

Manganese binding site 4 out of 5 in 4peg

Go back to Manganese Binding Sites List in 4peg
Manganese binding site 4 out of 5 in the DBR1 in Complex with Guanosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of DBR1 in Complex with Guanosine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:30.9
occ:1.00
O D:HOH712 2.1 39.3 1.0
OD1 D:ASN90 2.1 30.9 1.0
O2P D:5GP402 2.2 43.7 1.0
NE2 D:HIS180 2.3 22.8 1.0
OD2 D:ASP45 2.3 27.9 1.0
ND1 D:HIS230 2.4 24.8 1.0
CG D:ASN90 3.1 31.5 1.0
CE1 D:HIS230 3.1 29.0 1.0
CG D:ASP45 3.2 26.0 1.0
CE1 D:HIS180 3.2 22.5 1.0
OD1 D:ASP45 3.3 30.4 1.0
CD2 D:HIS180 3.3 25.2 1.0
P D:5GP402 3.3 44.5 1.0
ND2 D:ASN90 3.4 34.1 1.0
O3P D:5GP402 3.5 41.0 1.0
CG D:HIS230 3.6 25.2 1.0
CA D:HIS230 3.8 32.0 1.0
CB D:HIS230 4.0 26.5 1.0
O5' D:5GP402 4.1 63.7 1.0
SG D:CYS14 4.1 71.9 1.0
O D:HIS230 4.3 35.3 1.0
ND1 D:HIS180 4.4 22.3 1.0
NE2 D:HIS230 4.4 30.6 1.0
N D:ASN90 4.4 21.9 1.0
CG D:HIS180 4.4 25.8 1.0
CB D:ASN90 4.5 24.9 1.0
CB D:ASP45 4.6 26.9 1.0
CD2 D:HIS91 4.6 35.4 1.0
CD2 D:HIS230 4.6 27.8 1.0
C D:HIS230 4.6 35.1 1.0
O1P D:5GP402 4.6 44.3 1.0
C5' D:5GP402 4.7 66.1 1.0
N D:HIS230 4.8 33.5 1.0
NE2 D:HIS91 5.0 34.2 1.0
CA D:ASN90 5.0 21.8 1.0

Manganese binding site 5 out of 5 in 4peg

Go back to Manganese Binding Sites List in 4peg
Manganese binding site 5 out of 5 in the DBR1 in Complex with Guanosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of DBR1 in Complex with Guanosine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:23.9
occ:1.00
OD1 E:ASN90 2.2 24.2 1.0
O E:HOH677 2.2 23.4 1.0
OD2 E:ASP45 2.2 18.1 1.0
NE2 E:HIS180 2.3 21.3 1.0
ND1 E:HIS230 2.4 20.3 1.0
O1P E:5GP402 2.5 31.9 1.0
CG E:ASP45 3.1 18.7 1.0
CE1 E:HIS230 3.2 22.6 1.0
CE1 E:HIS180 3.2 21.9 1.0
CG E:ASN90 3.2 22.1 1.0
OD1 E:ASP45 3.3 15.6 1.0
CD2 E:HIS180 3.3 15.4 1.0
O2P E:5GP402 3.4 35.5 1.0
P E:5GP402 3.5 36.6 1.0
CG E:HIS230 3.6 21.3 1.0
ND2 E:ASN90 3.7 24.6 1.0
CA E:HIS230 3.9 28.7 1.0
CB E:HIS230 4.0 24.7 1.0
O E:HIS230 4.2 23.6 1.0
ND1 E:HIS180 4.4 14.1 1.0
NE2 E:HIS230 4.4 25.1 1.0
CG E:HIS180 4.4 17.2 1.0
SG E:CYS14 4.4 35.4 0.5
CB E:ASP45 4.4 20.4 1.0
O5' E:5GP402 4.5 48.9 1.0
N E:ASN90 4.5 17.5 1.0
C5' E:5GP402 4.5 52.4 1.0
CB E:ASN90 4.5 14.6 1.0
C E:HIS230 4.6 27.8 1.0
CD2 E:HIS230 4.6 22.1 1.0
O3P E:5GP402 4.7 37.5 1.0
N E:HIS230 4.7 34.1 1.0
CD2 E:HIS91 4.7 29.1 1.0

Reference:

E.J.Montemayor, A.Katolik, N.E.Clark, A.B.Taylor, J.P.Schuermann, D.J.Combs, R.Johnsson, S.P.Holloway, S.W.Stevens, M.J.Damha, P.J.Hart. Structural Basis of Lariat Rna Recognition By the Intron Debranching Enzyme DBR1. Nucleic Acids Res. V. 42 10845 2014.
ISSN: ESSN 1362-4962
PubMed: 25123664
DOI: 10.1093/NAR/GKU725
Page generated: Tue Dec 15 04:26:06 2020

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