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Manganese in PDB 3psn: Crystal Structure of Mouse VPS29 Complexed with MN2+

Enzymatic activity of Crystal Structure of Mouse VPS29 Complexed with MN2+

All present enzymatic activity of Crystal Structure of Mouse VPS29 Complexed with MN2+:
3.1.3.3;

Protein crystallography data

The structure of Crystal Structure of Mouse VPS29 Complexed with MN2+, PDB code: 3psn was solved by J.Swarbrick, D.Shaw, S.Chhabra, R.Ghai, E.Valkov, S.Norwood, B.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.17 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.437, 69.122, 69.024, 90.00, 105.44, 90.00
R / Rfree (%) 19.5 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Mouse VPS29 Complexed with MN2+ (pdb code 3psn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Mouse VPS29 Complexed with MN2+, PDB code: 3psn:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3psn

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Manganese binding site 1 out of 6 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


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 Mouse VPS29 Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:39.0
occ:1.00
 NE2 A:HIS117 2.1 27.1 1.0
NE2 A:HIS10 2.2 42.3 1.0
OD1 A:ASN39 2.3 31.0 1.0
OD1 A:ASP8 2.3 36.7 1.0
O A:HOH183 2.5 37.2 1.0
CG A:ASP8 3.0 35.6 1.0
CE1 A:HIS117 3.1 36.8 1.0
CE1 A:HIS10 3.1 39.6 1.0
CD2 A:HIS117 3.2 35.1 1.0
MN A:MN602 3.2 42.0 1.0
CG A:ASN39 3.3 41.2 1.0
CD2 A:HIS10 3.3 40.6 1.0
CB A:ASP8 3.5 28.4 1.0
CB A:ASN39 3.6 44.7 1.0
OD2 A:ASP8 4.0 31.6 1.0
CE1 A:HIS86 4.1 31.6 1.0
CA A:ASP8 4.1 30.9 1.0
O A:HIS115 4.1 36.1 1.0
ND1 A:HIS117 4.2 37.2 1.0
ND1 A:HIS10 4.3 45.0 1.0
CG A:HIS117 4.3 34.5 1.0
NE2 A:HIS86 4.3 43.7 1.0
CG A:HIS10 4.4 44.4 1.0
ND2 A:ASN39 4.5 27.9 1.0
CA A:HIS115 4.5 42.2 1.0
C A:HIS115 4.7 33.5 1.0
ND1 A:HIS115 4.9 38.0 1.0
OD1 A:ASP62 4.9 42.2 1.0
C A:ASP8 5.0 35.2 1.0

Manganese binding site 2 out of 6 in 3psn

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Manganese binding site 2 out of 6 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


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 Mouse VPS29 Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:42.0
occ:1.00
 O A:HOH183 2.1 37.2 1.0
OD1 A:ASP62 2.2 42.2 1.0
NE2 A:HIS86 2.2 43.7 1.0
ND1 A:HIS115 2.3 38.0 1.0
OD1 A:ASN39 2.5 31.0 1.0
CG A:ASP62 2.9 53.3 1.0
OD2 A:ASP62 2.9 56.1 1.0
CE1 A:HIS115 3.0 42.0 1.0
CE1 A:HIS86 3.1 31.6 1.0
MN A:MN601 3.2 39.0 1.0
CD2 A:HIS86 3.3 33.6 1.0
CG A:ASN39 3.5 41.2 1.0
CG A:HIS115 3.5 38.5 1.0
CA A:HIS115 3.9 42.2 1.0
OD1 A:ASP8 4.0 36.7 1.0
ND2 A:ASN39 4.0 27.9 1.0
CB A:HIS115 4.0 31.2 1.0
NE2 A:HIS115 4.2 50.9 1.0
ND1 A:HIS86 4.2 30.6 1.0
CB A:ASP62 4.3 38.5 1.0
O A:HIS115 4.3 36.1 1.0
CG A:HIS86 4.4 32.3 1.0
N A:ASP62 4.5 40.3 1.0
CD2 A:HIS115 4.5 42.3 1.0
C A:HIS115 4.6 33.5 1.0
CB A:ASN39 4.7 44.7 1.0
CB A:HIS88 4.8 33.3 1.0
NE2 A:HIS10 4.8 42.3 1.0
N A:HIS115 4.9 29.9 1.0
NE2 A:HIS117 4.9 27.1 1.0
CE1 A:HIS10 5.0 39.6 1.0
CA A:ASP62 5.0 41.2 1.0
O A:ASP62 5.0 55.9 1.0

Manganese binding site 3 out of 6 in 3psn

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Manganese binding site 3 out of 6 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


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 Mouse VPS29 Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:66.0
occ:1.00
 OE2 A:GLU123 2.3 51.8 1.0
O A:LYS180 2.4 51.1 1.0
CD A:GLU123 3.1 54.2 1.0
OE1 A:GLU123 3.1 49.1 1.0
C A:LYS180 3.5 51.0 1.0
N A:LYS180 3.9 42.6 1.0
CA A:LYS180 4.1 50.1 1.0
CB A:LYS180 4.4 59.2 1.0
O A:HOH207 4.4 47.5 1.0
OD1 A:ASN126 4.5 52.5 1.0
CD1 A:TYR179 4.5 31.7 1.0
CG A:GLU123 4.5 41.9 1.0
OG A:SER182 4.6 74.0 1.0
N A:LYS181 4.6 46.2 1.0
CE1 A:TYR179 4.7 34.5 1.0
CA A:LYS181 4.9 54.1 1.0
CG A:LYS180 5.0 76.4 1.0

Manganese binding site 4 out of 6 in 3psn

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Manganese binding site 4 out of 6 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


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 Mouse VPS29 Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:37.6
occ:1.00
 NE2 B:HIS117 2.0 32.8 1.0
OD1 B:ASP8 2.2 34.6 1.0
NE2 B:HIS10 2.3 41.2 1.0
O B:HOH183 2.3 38.3 1.0
OD1 B:ASN39 2.4 33.4 1.0
CE1 B:HIS117 3.0 38.8 1.0
CG B:ASP8 3.0 33.4 1.0
CD2 B:HIS117 3.1 35.3 1.0
CE1 B:HIS10 3.2 37.9 1.0
CD2 B:HIS10 3.3 41.5 1.0
MN B:MN702 3.3 41.2 1.0
CG B:ASN39 3.4 42.0 1.0
CB B:ASP8 3.5 31.4 1.0
CB B:ASN39 3.8 44.6 1.0
OD2 B:ASP8 4.0 33.1 1.0
O B:HIS115 4.0 38.3 1.0
CE1 B:HIS86 4.1 30.6 1.0
ND1 B:HIS117 4.1 36.0 1.0
CA B:ASP8 4.2 30.4 1.0
CG B:HIS117 4.2 31.6 1.0
NE2 B:HIS86 4.3 39.1 1.0
ND1 B:HIS10 4.3 43.1 1.0
CG B:HIS10 4.4 41.4 1.0
CA B:HIS115 4.5 39.2 1.0
ND2 B:ASN39 4.6 29.2 1.0
C B:HIS115 4.6 32.9 1.0
ND1 B:HIS115 4.8 36.6 1.0
N B:HIS115 5.0 28.3 1.0

Manganese binding site 5 out of 6 in 3psn

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Manganese binding site 5 out of 6 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


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 Mouse VPS29 Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:41.2
occ:1.00
 OD1 B:ASP62 2.2 44.6 1.0
ND1 B:HIS115 2.2 36.6 1.0
NE2 B:HIS86 2.2 39.1 1.0
O B:HOH183 2.3 38.3 1.0
OD1 B:ASN39 2.6 33.4 1.0
CE1 B:HIS115 2.9 42.1 1.0
CG B:ASP62 2.9 52.8 1.0
OD2 B:ASP62 2.9 61.4 1.0
CE1 B:HIS86 3.1 30.6 1.0
CD2 B:HIS86 3.2 32.1 1.0
MN B:MN701 3.3 37.6 1.0
CG B:HIS115 3.4 34.7 1.0
CG B:ASN39 3.6 42.0 1.0
CA B:HIS115 3.9 39.2 1.0
CB B:HIS115 4.0 30.6 1.0
OD1 B:ASP8 4.0 34.6 1.0
ND2 B:ASN39 4.1 29.2 1.0
NE2 B:HIS115 4.1 46.0 1.0
ND1 B:HIS86 4.3 31.1 1.0
CB B:ASP62 4.3 43.3 1.0
O B:HIS115 4.3 38.3 1.0
CG B:HIS86 4.3 32.8 1.0
CD2 B:HIS115 4.4 39.5 1.0
N B:ASP62 4.5 45.9 1.0
C B:HIS115 4.6 32.9 1.0
CB B:HIS88 4.7 32.5 1.0
N B:HIS115 4.8 28.3 1.0
CB B:ASN39 4.8 44.6 1.0
NE2 B:HIS117 4.9 32.8 1.0
NE2 B:HIS10 5.0 41.2 1.0
CA B:ASP62 5.0 44.1 1.0

Manganese binding site 6 out of 6 in 3psn

Go back to Manganese Binding Sites List in 3psn
Manganese binding site 6 out of 6 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


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 Mouse VPS29 Complexed with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn703

b:65.6
occ:1.00
 OE2 B:GLU123 2.1 52.3 1.0
O B:LYS180 2.4 50.7 1.0
CD B:GLU123 2.9 52.5 1.0
OE1 B:GLU123 3.0 46.1 1.0
C B:LYS180 3.5 50.4 1.0
N B:LYS180 3.9 44.7 1.0
CA B:LYS180 4.1 52.5 1.0
CG B:GLU123 4.4 40.2 1.0
CD1 B:TYR179 4.4 35.0 1.0
CB B:LYS180 4.4 59.9 1.0
OD1 B:ASN126 4.5 54.4 1.0
CE1 B:TYR179 4.6 31.6 1.0
N B:LYS181 4.7 48.1 1.0
OG B:SER182 4.7 71.5 1.0
CA B:LYS181 5.0 54.6 1.0

Reference:

J.Swarbrick, D.Shaw, S.Chhabra, R.Ghai, E.Valkov, S.Norwood, B.Collins. Conformational Dynamics and Biomolecular Interactions of VPS29 Studied By uc(Nmr) and X-Ray Crystallography To Be Published.
Page generated: Sat Oct 5 17:32:13 2024

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