Sodium in PDB 7lcz: Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn

Enzymatic activity of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn

All present enzymatic activity of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn:
3.2.2.6;

Protein crystallography data

The structure of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn, PDB code: 7lcz was solved by W.Gu, J.D.Nanson, Z.Luo, X.Jia, M.K.Manik, T.Ve, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.67 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.921, 50.788, 76.054, 103.52, 101.9, 95.26
R / Rfree (%) 21.2 / 23

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn (pdb code 7lcz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn, PDB code: 7lcz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7lcz

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Sodium binding site 1 out of 5 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:34.6
occ:1.00
 O A:HOH848 2.8 26.9 1.0
ND1 A:HIS392 2.9 22.6 1.0
O A:HOH809 3.0 32.4 1.0
HZ3 A:TRP385 3.0 26.3 1.0
HB2 A:HIS599 3.1 26.5 1.0
HA A:HIS392 3.2 23.6 1.0
HB2 A:HIS392 3.3 27.9 1.0
HB3 A:HIS599 3.5 26.5 1.0
HN72 A:NMN701 3.6 21.4 0.5
HN72 A:NMN701 3.6 21.4 0.5
O3P A:NMN701 3.7 21.4 0.5
N7 A:NMN701 3.7 21.4 0.5
N7 A:NMN701 3.7 21.4 0.5
CZ3 A:TRP385 3.7 15.2 1.0
CG A:HIS392 3.7 22.4 1.0
CB A:HIS599 3.7 16.7 1.0
O A:HOH1004 3.8 39.5 1.0
CB A:HIS392 3.8 21.8 1.0
HN71 A:NMN701 3.8 21.4 0.5
HN71 A:NMN701 3.8 21.4 0.5
CE1 A:HIS392 3.9 22.6 1.0
O1P A:NMN701 3.9 21.4 0.5
CA A:HIS392 3.9 19.5 1.0
HD2 A:HIS599 4.0 23.7 1.0
HE1 A:HIS392 4.1 48.9 1.0
HH2 A:TRP385 4.1 27.0 1.0
C7 A:NMN701 4.2 21.4 0.5
H1PO A:NMN701 4.2 21.4 0.5
C7 A:NMN701 4.3 21.4 0.5
CH2 A:TRP385 4.3 14.6 1.0
CG A:HIS599 4.3 16.7 1.0
HC2 A:NMN701 4.4 21.4 0.5
HC2 A:NMN701 4.4 21.4 0.5
CD2 A:HIS599 4.4 16.9 1.0
O A:HOH959 4.4 32.8 1.0
O2P A:NMN701 4.5 21.4 0.5
O A:HIS392 4.5 17.8 1.0
CE3 A:TRP385 4.6 14.9 1.0
HE3 A:TRP385 4.6 20.9 1.0
C3 A:NMN701 4.7 21.4 0.5
HB3 A:HIS392 4.7 27.9 1.0
C A:HIS392 4.7 18.5 1.0
C2 A:NMN701 4.7 21.4 0.5
O A:HIS599 4.7 17.4 1.0
C3 A:NMN701 4.7 21.4 0.5
C2 A:NMN701 4.8 21.4 0.5
O7 A:NMN701 4.8 21.4 0.5
O A:GLY600 4.8 17.8 1.0
P A:NMN701 4.9 21.4 0.5
O7 A:NMN701 4.9 21.4 0.5
CD2 A:HIS392 4.9 22.4 1.0
HE22 A:GLN638 5.0 42.4 1.0
NE2 A:HIS392 5.0 22.4 1.0

Sodium binding site 2 out of 5 in 7lcz

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Sodium binding site 2 out of 5 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:34.9
occ:1.00
 H22 A:EDO702 2.3 26.3 1.0
H21 A:EDO702 2.3 26.3 1.0
O A:ALA591 2.3 35.6 1.0
H A:ASN594 2.5 49.0 1.0
O A:ASN594 2.7 37.2 1.0
C2 A:EDO702 2.7 26.3 1.0
C A:ALA591 3.0 36.0 1.0
HA A:ALA598 3.0 27.8 1.0
HB3 A:ASN594 3.2 46.1 1.0
N A:ASN594 3.2 38.3 1.0
HA A:ALA591 3.2 45.3 1.0
HB2 A:HIS597 3.3 37.6 1.0
H A:SER593 3.4 46.0 1.0
O A:PHE590 3.5 23.5 1.0
C A:HIS597 3.5 23.8 1.0
C A:ASN594 3.5 37.6 1.0
O A:HIS597 3.5 23.9 1.0
N A:ALA598 3.6 16.8 1.0
HG A:SER593 3.6 47.6 1.0
CA A:ALA591 3.6 36.2 1.0
O2 A:EDO702 3.7 26.3 1.0
HO2 A:EDO702 3.7 26.3 1.0
N A:SER593 3.7 36.7 1.0
CA A:ASN594 3.7 38.2 1.0
CA A:ALA598 3.7 16.9 1.0
H A:HIS597 3.8 36.3 1.0
N A:ARG592 3.8 37.9 1.0
HA A:ARG592 3.8 41.5 1.0
O1 A:EDO702 3.9 26.3 1.0
CB A:ASN594 3.9 38.6 1.0
C1 A:EDO702 3.9 26.3 1.0
H A:ALA598 4.0 26.7 1.0
C A:ARG592 4.0 38.2 1.0
HB2 A:ALA598 4.1 33.7 1.0
CA A:ARG592 4.1 37.9 1.0
CB A:HIS597 4.1 23.7 1.0
CA A:HIS597 4.2 23.9 1.0
C A:SER593 4.2 37.1 1.0
O A:HOH887 4.2 25.1 1.0
OG A:SER593 4.3 37.6 1.0
N A:HIS597 4.4 23.9 1.0
C A:PHE590 4.4 23.6 1.0
HB3 A:HIS597 4.4 37.6 1.0
CA A:SER593 4.5 37.2 1.0
HB2 A:ASN594 4.5 46.1 1.0
H A:ARG592 4.5 38.3 1.0
CB A:ALA598 4.5 17.1 1.0
H11 A:EDO702 4.5 26.3 1.0
N A:ALA591 4.5 36.8 1.0
HB1 A:ALA591 4.6 52.6 1.0
HA A:ASN594 4.7 51.1 1.0
H12 A:EDO702 4.7 26.3 1.0
N A:LEU595 4.7 22.7 1.0
O A:ARG592 4.7 38.3 1.0
CB A:ALA591 4.8 36.2 1.0
HO1 A:EDO702 4.8 26.3 1.0
HB1 A:ALA598 4.9 33.7 1.0
C A:ALA598 4.9 17.3 1.0
CB A:SER593 5.0 37.7 1.0
CG A:ASN594 5.0 38.5 1.0
HA A:LEU595 5.0 43.3 1.0

Sodium binding site 3 out of 5 in 7lcz

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Sodium binding site 3 out of 5 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:36.3
occ:1.00
 O B:HOH882 2.4 33.6 1.0
HG1 B:THR500 2.9 47.0 1.0
SD B:MET461 3.0 28.6 1.0
HG B:SER464 3.1 63.9 1.0
O B:HOH871 3.1 41.1 1.0
OG1 B:THR500 3.1 21.4 1.0
HB B:THR500 3.6 35.4 1.0
HE1 B:MET461 3.6 60.2 1.0
HB2 B:SER464 3.7 50.6 1.0
OE1 B:GLU497 3.8 17.6 1.0
OG B:SER464 3.9 28.7 1.0
CB B:THR500 3.9 21.8 1.0
CE B:MET461 3.9 30.7 1.0
HB3 B:SER464 3.9 50.6 1.0
HA B:MET461 4.0 36.8 1.0
O B:HOH1065 4.0 33.6 1.0
O B:HOH893 4.0 28.6 1.0
CB B:SER464 4.1 27.4 1.0
HE2 B:MET461 4.2 60.2 1.0
HB2 B:ASP502 4.5 29.8 1.0
HG23 B:THR500 4.5 34.1 1.0
HG21 B:THR505 4.5 32.0 1.0
HB3 B:ASP502 4.6 29.8 1.0
CG B:MET461 4.6 29.4 1.0
CG2 B:THR500 4.7 21.4 1.0
HE3 B:MET461 4.7 60.2 1.0
CD B:GLU497 4.7 18.2 1.0
OE2 B:GLU497 4.8 18.9 1.0
HG3 B:MET461 4.8 39.8 1.0
CA B:MET461 4.9 29.3 1.0
HG22 B:THR500 4.9 34.1 1.0
O B:HOH837 4.9 36.0 1.0
HA B:THR500 5.0 25.3 1.0
OG1 B:THR505 5.0 15.5 1.0
HB2 B:MET461 5.0 46.7 1.0

Sodium binding site 4 out of 5 in 7lcz

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Sodium binding site 4 out of 5 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:36.3
occ:1.00
 NA B:NA704 2.7 36.3 1.0
HH21 B:ARG383 3.0 65.1 1.0
O B:HOH866 3.1 33.6 1.0
HB3 B:ARG383 3.2 39.2 1.0
NH2 B:ARG383 3.3 43.3 1.0
HE B:ARG383 3.5 70.6 1.0
HH22 B:ARG383 3.7 65.1 1.0
CZ B:ARG383 3.8 41.6 1.0
NE B:ARG383 3.8 39.8 1.0
HG22 B:VAL387 4.1 40.4 1.0
CB B:ARG383 4.2 35.2 1.0
O B:ARG383 4.3 34.4 1.0
HG2 B:ARG383 4.5 54.0 1.0
HB2 B:ARG383 4.6 39.2 1.0
NH1 B:ARG383 4.7 41.9 1.0
CG B:ARG383 4.8 36.8 1.0
HG23 B:VAL387 4.8 40.4 1.0
HA B:ARG383 4.8 41.0 1.0
CG2 B:VAL387 4.8 32.7 1.0
C B:ARG383 4.9 33.3 1.0
CD B:ARG383 4.9 37.9 1.0
CA B:ARG383 4.9 34.0 1.0
HH12 B:ARG383 4.9 80.5 1.0

Sodium binding site 5 out of 5 in 7lcz

Go back to Sodium Binding Sites List in 7lcz
Sodium binding site 5 out of 5 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Nmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na704

b:36.3
occ:1.00
 NA B:NA703 2.7 36.3 1.0
O B:ARG383 2.8 34.4 1.0
HB3 B:ALA386 3.0 42.5 1.0
HG22 B:VAL387 3.0 40.4 1.0
HB3 B:ARG383 3.4 39.2 1.0
HG23 B:VAL387 3.5 40.4 1.0
HA B:ARG383 3.6 41.0 1.0
CG2 B:VAL387 3.7 32.7 1.0
C B:ARG383 3.8 33.3 1.0
HA B:VAL387 3.8 45.4 1.0
N B:VAL387 3.8 32.4 1.0
CB B:ALA386 3.8 33.6 1.0
H B:VAL387 3.9 41.7 1.0
HB1 B:ALA386 4.0 42.5 1.0
C B:ALA386 4.0 34.0 1.0
CA B:ARG383 4.0 34.0 1.0
CB B:ARG383 4.2 35.2 1.0
CA B:VAL387 4.2 33.7 1.0
HG21 B:VAL387 4.4 40.4 1.0
O B:ALA386 4.4 35.8 1.0
CA B:ALA386 4.4 32.7 1.0
HG2 B:ARG383 4.5 54.0 1.0
H B:ALA386 4.5 43.5 1.0
HB2 B:ALA386 4.6 42.5 1.0
CB B:VAL387 4.6 33.1 1.0
N B:ALA386 4.8 30.8 1.0
O B:HOH866 4.9 33.6 1.0
CG B:ARG383 4.9 36.8 1.0
HB2 B:ARG383 4.9 39.2 1.0
HD3 B:PRO388 5.0 70.6 1.0
N B:ALA384 5.0 27.5 1.0

Reference:

M.Figley, W.Gu, J.D.Nanson, Y.Shi, Y.Sasaki, K.Cunnea, A.K.Malde, X.Jia, Z.Luo, F.Saikot, T.Mosaiab, V.Masic, S.Holt, L.Hartley-Tassell, H.Y.Mcguinness, M.K.Manik, T.Bosanac, M.J.Landsberg, P.S.Kerry, M.Mobli, R.O.Hughes, J.Milbrandt, B.Kobe, A.Diantonio, T.Ve. SARM1 Is A Metabolic Sensor Activated By An Increased Nmn/Nad+ Ratio to Trigger Axon Degeneration Neuron 2021.
ISSN: ISSN 0896-6273
DOI: 10.1016/J.NEURON.2021.02.009
Page generated: Tue Oct 8 17:34:41 2024

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