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Manganese in PDB 4ic1: Crystal Structure of SSO0001

Protein crystallography data

The structure of Crystal Structure of SSO0001, PDB code: 4ic1 was solved by B.Nocek, T.Skarina, S.Lemak, N.Beloglazova, R.Flick, G.Brown, A.Savchenko, A.Joachimiak, A.F.Yakunin, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.152, 197.761, 89.410, 90.00, 100.88, 90.00
R / Rfree (%) 20.1 / 24.9

Other elements in 4ic1:

The structure of Crystal Structure of SSO0001 also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of SSO0001 (pdb code 4ic1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Crystal Structure of SSO0001, PDB code: 4ic1:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4ic1

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Manganese binding site 1 out of 10 in the Crystal Structure of SSO0001


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:32.4
occ:0.99
 OE1 A:GLU113 2.2 22.1 1.0
NE2 A:HIS62 2.3 18.5 1.0
O A:ILE114 2.3 16.1 1.0
OD2 A:ASP99 2.4 13.4 1.0
O A:HOH444 2.6 17.1 1.0
CD A:GLU113 3.2 19.4 1.0
CG A:ASP99 3.2 11.4 1.0
CE1 A:HIS62 3.2 18.0 1.0
CD2 A:HIS62 3.4 19.1 1.0
OD1 A:ASP99 3.4 9.8 1.0
C A:ILE114 3.4 15.1 1.0
N A:ILE114 3.6 14.4 1.0
NZ A:LYS115 3.9 10.8 1.0
OE2 A:GLU113 3.9 17.7 1.0
CA A:ILE114 4.0 14.7 1.0
O A:HOH446 4.1 22.9 1.0
CG A:GLU113 4.2 18.6 1.0
CD A:LYS115 4.2 11.5 1.0
O A:HOH438 4.3 20.5 0.9
CE A:LYS115 4.4 11.2 1.0
ND1 A:HIS62 4.4 17.1 1.0
CB A:ILE114 4.4 14.7 1.0
CG A:HIS62 4.5 17.2 1.0
C A:GLU113 4.5 14.4 1.0
N A:LYS115 4.6 15.5 1.0
CB A:ASP99 4.6 11.6 1.0
CA A:GLU113 4.8 14.4 1.0
CA A:LYS115 4.9 14.9 1.0
O A:HOH445 4.9 2.0 1.0

Manganese binding site 2 out of 10 in 4ic1

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Manganese binding site 2 out of 10 in the Crystal Structure of SSO0001


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 SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:26.9
occ:0.99
 OE1 B:GLU113 2.2 15.9 1.0
OD2 B:ASP99 2.3 17.0 1.0
NE2 B:HIS62 2.4 13.6 1.0
O B:ILE114 2.4 13.9 1.0
O B:HOH459 2.5 13.5 1.0
CD B:GLU113 3.2 16.5 1.0
CG B:ASP99 3.2 11.6 1.0
CD2 B:HIS62 3.3 15.1 1.0
OD1 B:ASP99 3.3 14.5 1.0
CE1 B:HIS62 3.4 13.2 1.0
C B:ILE114 3.5 13.2 1.0
OE2 B:GLU113 3.7 17.4 1.0
N B:ILE114 3.8 11.0 1.0
CD B:LYS115 4.0 12.6 1.0
NZ B:LYS115 4.1 11.6 1.0
CA B:ILE114 4.1 11.6 1.0
O B:HOH401 4.2 20.0 1.0
CB B:ILE114 4.2 11.8 1.0
O B:HOH408 4.3 13.8 1.0
CG B:GLU113 4.3 12.8 1.0
CG B:HIS62 4.5 13.2 1.0
ND1 B:HIS62 4.5 14.2 1.0
CE B:LYS115 4.6 10.4 1.0
CB B:ASP99 4.6 8.8 1.0
N B:LYS115 4.6 13.6 1.0
C B:GLU113 4.6 10.0 1.0
CA B:LYS115 4.8 13.9 1.0
O B:HOH456 4.9 6.3 1.0
CA B:GLU113 4.9 8.9 1.0
CG1 B:ILE114 5.0 14.4 1.0

Manganese binding site 3 out of 10 in 4ic1

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Manganese binding site 3 out of 10 in the Crystal Structure of SSO0001


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 SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:37.0
occ:0.80
 OE2 C:GLU113 2.2 29.2 1.0
O C:ILE114 2.4 22.9 1.0
OD2 C:ASP99 2.4 17.2 1.0
NE2 C:HIS62 2.4 23.9 1.0
CG C:ASP99 3.2 18.9 1.0
CD C:GLU113 3.3 30.2 1.0
CE1 C:HIS62 3.3 25.2 1.0
OD1 C:ASP99 3.3 21.5 1.0
CD2 C:HIS62 3.4 23.7 1.0
C C:ILE114 3.5 22.8 1.0
N C:ILE114 3.8 23.1 1.0
NZ C:LYS115 3.8 24.1 1.0
CD C:LYS115 4.0 20.3 1.0
OE1 C:GLU113 4.0 33.0 1.0
CA C:ILE114 4.2 23.0 1.0
CG C:GLU113 4.2 27.2 1.0
O C:HOH418 4.2 21.6 1.0
ND1 C:HIS62 4.4 25.8 1.0
CB C:ILE114 4.5 23.5 1.0
CE C:LYS115 4.5 21.5 1.0
CG C:HIS62 4.5 23.7 1.0
N C:LYS115 4.6 22.3 1.0
CB C:ASP99 4.7 20.2 1.0
C C:GLU113 4.8 23.8 1.0
CA C:LYS115 4.8 21.2 1.0
O C:HOH422 4.9 19.1 1.0

Manganese binding site 4 out of 10 in 4ic1

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Manganese binding site 4 out of 10 in the Crystal Structure of SSO0001


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 SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:19.9
occ:0.80
 OD2 D:ASP99 2.2 15.4 1.0
OE2 D:GLU113 2.2 22.2 1.0
O D:HOH441 2.3 12.5 1.0
NE2 D:HIS62 2.4 19.1 1.0
O D:ILE114 2.5 17.0 1.0
CG D:ASP99 3.1 13.3 1.0
OD1 D:ASP99 3.2 16.0 1.0
CD D:GLU113 3.2 22.0 1.0
CE1 D:HIS62 3.4 21.9 1.0
CD2 D:HIS62 3.4 18.3 1.0
C D:ILE114 3.6 15.8 1.0
N D:ILE114 3.8 13.3 1.0
O D:HOH428 3.8 31.0 1.0
NZ D:LYS115 3.9 20.3 1.0
CD D:LYS115 3.9 20.4 1.0
OE1 D:GLU113 4.0 23.1 1.0
O D:HOH442 4.0 20.1 1.0
CG D:GLU113 4.2 18.9 1.0
CA D:ILE114 4.2 14.2 1.0
CE D:LYS115 4.5 18.4 1.0
CB D:ASP99 4.5 11.2 1.0
ND1 D:HIS62 4.5 20.8 1.0
CB D:ILE114 4.5 15.1 1.0
CG D:HIS62 4.6 16.1 1.0
N D:LYS115 4.7 16.3 1.0
C D:GLU113 4.7 12.7 1.0
O D:HOH439 4.9 9.9 1.0
CA D:LYS115 4.9 16.2 1.0
CA D:GLU113 4.9 12.0 1.0

Manganese binding site 5 out of 10 in 4ic1

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Manganese binding site 5 out of 10 in the Crystal Structure of SSO0001


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn301

b:35.4
occ:0.80
 OE1 F:GLU113 2.2 32.7 1.0
O F:ILE114 2.3 32.1 1.0
O F:HOH419 2.3 26.4 1.0
OD2 F:ASP99 2.5 32.2 1.0
NE2 F:HIS62 2.6 37.7 1.0
CG F:ASP99 3.3 34.5 1.0
OD1 F:ASP99 3.3 34.6 1.0
CE1 F:HIS62 3.3 38.1 1.0
CD F:GLU113 3.4 35.1 1.0
C F:ILE114 3.5 32.6 1.0
CD2 F:HIS62 3.6 36.1 1.0
N F:ILE114 3.9 30.0 1.0
NZ F:LYS115 4.1 36.8 1.0
O F:HOH403 4.1 29.7 1.0
CD F:LYS115 4.1 35.5 1.0
CG F:GLU113 4.1 33.8 1.0
CE F:LYS115 4.2 35.9 1.0
CA F:ILE114 4.2 31.0 1.0
OE2 F:GLU113 4.3 37.6 1.0
CB F:ILE114 4.5 31.3 1.0
ND1 F:HIS62 4.5 36.6 1.0
N F:LYS115 4.6 34.2 1.0
CG F:HIS62 4.7 34.5 1.0
CB F:ASP99 4.8 33.7 1.0
C F:GLU113 4.8 29.7 1.0
CA F:LYS115 4.9 35.5 1.0
CG F:LYS115 5.0 35.7 1.0

Manganese binding site 6 out of 10 in 4ic1

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Manganese binding site 6 out of 10 in the Crystal Structure of SSO0001


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn301

b:25.5
occ:0.60
 OE2 G:GLU113 2.1 23.6 1.0
NE2 G:HIS62 2.2 35.5 1.0
OD2 G:ASP99 2.4 28.3 1.0
O G:HOH421 2.4 26.8 1.0
O G:ILE114 2.5 30.4 1.0
CE1 G:HIS62 3.1 36.2 1.0
CD G:GLU113 3.1 29.3 1.0
CG G:ASP99 3.1 30.0 1.0
OD1 G:ASP99 3.2 33.3 1.0
CD2 G:HIS62 3.2 33.9 1.0
C G:ILE114 3.7 28.5 1.0
OE1 G:GLU113 3.8 31.4 1.0
O G:HOH420 3.9 26.2 1.0
N G:ILE114 4.0 26.0 1.0
ND1 G:HIS62 4.2 35.1 1.0
CG G:GLU113 4.3 27.5 1.0
NZ G:LYS115 4.3 27.8 1.0
CG G:HIS62 4.3 31.5 1.0
CA G:ILE114 4.3 27.4 1.0
CD G:LYS115 4.4 28.6 1.0
CB G:ILE114 4.5 28.0 1.0
CE G:LYS115 4.5 29.4 1.0
CB G:ASP99 4.6 28.3 1.0
O G:HOH402 4.7 12.8 1.0
N G:LYS115 4.7 28.0 1.0
C G:GLU113 4.9 25.3 1.0
CA G:LYS115 5.0 28.1 1.0

Manganese binding site 7 out of 10 in 4ic1

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Manganese binding site 7 out of 10 in the Crystal Structure of SSO0001


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn301

b:34.3
occ:0.80
 OE2 H:GLU113 2.2 26.3 1.0
O H:HOH426 2.3 34.7 1.0
O H:ILE114 2.3 21.8 1.0
NE2 H:HIS62 2.4 30.8 1.0
OD2 H:ASP99 2.4 20.7 1.0
CD H:GLU113 3.2 29.4 1.0
CG H:ASP99 3.2 21.3 1.0
CE1 H:HIS62 3.3 31.5 1.0
OD1 H:ASP99 3.4 22.6 1.0
CD2 H:HIS62 3.4 32.3 1.0
C H:ILE114 3.4 22.2 1.0
N H:ILE114 3.6 22.4 1.0
OE1 H:GLU113 3.9 31.9 1.0
CA H:ILE114 4.0 21.3 1.0
NZ H:LYS115 4.1 23.2 1.0
CB H:ILE114 4.2 21.3 1.0
CG H:GLU113 4.2 27.4 1.0
CE H:LYS115 4.3 23.8 1.0
CD H:LYS115 4.3 23.5 1.0
ND1 H:HIS62 4.4 33.6 1.0
CG H:HIS62 4.5 32.8 1.0
C H:GLU113 4.5 23.9 1.0
N H:LYS115 4.6 22.0 1.0
CB H:ASP99 4.6 20.1 1.0
CA H:GLU113 4.8 24.6 1.0
O H:HOH423 4.8 20.0 1.0
CA H:LYS115 5.0 22.5 1.0

Manganese binding site 8 out of 10 in 4ic1

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Manganese binding site 8 out of 10 in the Crystal Structure of SSO0001


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn301

b:45.9
occ:0.60
 OE2 I:GLU113 2.1 49.9 1.0
OD2 I:ASP99 2.6 52.8 1.0
O I:ILE114 2.9 41.4 1.0
NE2 I:HIS62 2.9 43.3 1.0
CD I:GLU113 3.2 50.0 1.0
CG I:ASP99 3.4 50.8 1.0
OD1 I:ASP99 3.4 54.2 1.0
CE1 I:HIS62 3.6 43.0 1.0
OE1 I:GLU113 3.9 52.3 1.0
NZ I:LYS115 4.0 48.5 1.0
CD2 I:HIS62 4.0 42.4 1.0
C I:ILE114 4.0 40.4 1.0
O I:HOH401 4.1 34.2 1.0
CG I:GLU113 4.2 46.3 1.0
N I:ILE114 4.2 40.5 1.0
CE I:LYS115 4.4 47.5 1.0
CD I:LYS115 4.4 45.2 1.0
CA I:ILE114 4.6 40.3 1.0
ND1 I:HIS62 4.8 42.8 1.0
CB I:ASP99 4.8 49.1 1.0
CB I:ILE114 4.9 40.6 1.0
CG I:HIS62 5.0 42.2 1.0

Manganese binding site 9 out of 10 in 4ic1

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Manganese binding site 9 out of 10 in the Crystal Structure of SSO0001


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn301

b:43.1
occ:0.70
 OE2 J:GLU113 2.1 32.6 1.0
OD2 J:ASP99 2.3 33.8 1.0
NE2 J:HIS62 2.3 40.3 1.0
O J:ILE114 2.5 36.2 1.0
CD J:GLU113 3.2 37.4 1.0
CE1 J:HIS62 3.2 42.4 1.0
CG J:ASP99 3.3 34.6 1.0
CD2 J:HIS62 3.4 40.5 1.0
OD1 J:ASP99 3.5 32.5 1.0
C J:ILE114 3.6 35.3 1.0
OE1 J:GLU113 3.9 37.6 1.0
N J:ILE114 4.0 35.9 1.0
NZ J:LYS115 4.2 34.5 1.0
CA J:ILE114 4.3 35.8 1.0
CG J:GLU113 4.3 38.0 1.0
CD J:LYS115 4.3 36.2 1.0
ND1 J:HIS62 4.4 41.0 1.0
CG J:HIS62 4.5 39.7 1.0
CB J:ILE114 4.5 36.0 1.0
O J:HOH402 4.6 9.7 0.9
N J:LYS115 4.6 34.4 1.0
CB J:ASP99 4.7 36.0 1.0
CE J:LYS115 4.7 36.4 1.0
CA J:LYS115 4.8 34.2 1.0
C J:GLU113 4.9 36.7 1.0

Manganese binding site 10 out of 10 in 4ic1

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Manganese binding site 10 out of 10 in the Crystal Structure of SSO0001


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of SSO0001 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mn301

b:28.4
occ:0.60
 OE2 K:GLU113 2.2 32.8 1.0
O K:ILE114 2.2 32.2 1.0
NE2 K:HIS62 2.4 37.0 1.0
OD2 K:ASP99 2.4 26.6 1.0
CE1 K:HIS62 3.2 38.6 1.0
CG K:ASP99 3.3 30.4 1.0
CD K:GLU113 3.3 36.9 1.0
OD1 K:ASP99 3.3 27.9 1.0
C K:ILE114 3.4 30.9 1.0
CD2 K:HIS62 3.5 37.5 1.0
NZ K:LYS115 3.8 28.5 1.0
N K:ILE114 3.8 31.0 1.0
CD K:LYS115 3.8 27.8 1.0
OE1 K:GLU113 4.0 36.9 1.0
CA K:ILE114 4.1 31.0 1.0
CG K:GLU113 4.3 35.0 1.0
ND1 K:HIS62 4.4 38.2 1.0
N K:LYS115 4.4 30.4 1.0
CE K:LYS115 4.4 27.4 1.0
CB K:ILE114 4.5 31.5 1.0
CG K:HIS62 4.6 36.3 1.0
C K:GLU113 4.6 31.0 1.0
CA K:LYS115 4.7 29.2 1.0
CB K:ASP99 4.7 32.1 1.0
CA K:GLU113 4.9 31.3 1.0
O K:HOH416 4.9 25.6 1.0

Reference:

S.Lemak, N.Beloglazova, B.Nocek, T.Skarina, R.Flick, G.Brown, A.Popovic, A.Joachimiak, A.Savchenko, A.F.Yakunin. Toroidal Structure and Dna Cleavage By the Crispr-Associated [4FE-4S] Cluster Containing CAS4 Nuclease SSO0001 From Sulfolobus Solfataricus. J.Am.Chem.Soc. V. 135 17476 2013.
ISSN: ISSN 0002-7863
PubMed: 24171432
DOI: 10.1021/JA408729B
Page generated: Sat Oct 5 19:47:25 2024

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